Pathway Analysis for MOFA (thresL criterion)
John Zhuang
2024-08-08
library(multiMiR)## Welcome to multiMiR.
##
## multiMiR database URL has been set to the
## default value: http://multimir.org/
##
## Database Version: 2.3.0 Updated: 2020-04-15library(clusterProfiler)## ## clusterProfiler v4.12.2 Learn more at https://yulab-smu.top/contribution-knowledge-mining/
##
## Please cite:
##
## Guangchuang Yu, Li-Gen Wang, Yanyan Han and Qing-Yu He.
## clusterProfiler: an R package for comparing biological themes among
## gene clusters. OMICS: A Journal of Integrative Biology 2012,
## 16(5):284-287##
## Attaching package: 'clusterProfiler'## The following object is masked from 'package:multiMiR':
##
## select## The following object is masked from 'package:stats':
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## filterlibrary(org.Hs.eg.db)## Loading required package: AnnotationDbi## Loading required package: stats4## Loading required package: BiocGenerics##
## Attaching package: 'BiocGenerics'## The following objects are masked from 'package:stats':
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## IQR, mad, sd, var, xtabs## The following objects are masked from 'package:base':
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## anyDuplicated, aperm, append, as.data.frame, basename, cbind,
## colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find,
## get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply,
## match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
## Position, rank, rbind, Reduce, rownames, sapply, setdiff, table,
## tapply, union, unique, unsplit, which.max, which.min## Loading required package: Biobase## Welcome to Bioconductor
##
## Vignettes contain introductory material; view with
## 'browseVignettes()'. To cite Bioconductor, see
## 'citation("Biobase")', and for packages 'citation("pkgname")'.## Loading required package: IRanges## Loading required package: S4Vectors##
## Attaching package: 'S4Vectors'## The following object is masked from 'package:clusterProfiler':
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## rename## The following object is masked from 'package:utils':
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## findMatches## The following objects are masked from 'package:base':
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## expand.grid, I, unname##
## Attaching package: 'IRanges'## The following object is masked from 'package:clusterProfiler':
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## slice## The following object is masked from 'package:grDevices':
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## windows##
## Attaching package: 'AnnotationDbi'## The following object is masked from 'package:clusterProfiler':
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## select## library(stringr)
library(ggplot2)0. Loading of Results
A. List of all Gene names in the dataset
gene.names = readRDS("data/derived/unique_gene_names.rds")B. Selected Features
results.mofa = readRDS("data/sel_features/results_mofa_extracted_by_bic.rds")
sel.features = results.mofa
sel.features## $`1f`
## $`1f`$Factor1
## hsa-mir-1185-1 hsa-mir-1185-2 hsa-mir-1193 hsa-mir-1197 hsa-mir-127
## -0.7629508 -0.7462546 -0.6264293 -0.8177493 -0.6107271
## hsa-mir-134 hsa-mir-136 hsa-mir-137 hsa-mir-154 hsa-mir-299
## -0.5900502 -0.6225595 0.3615164 -0.6243017 -0.6020226
## hsa-mir-323 hsa-mir-323b hsa-mir-329-1 hsa-mir-329-2 hsa-mir-337
## -0.7085735 -0.7171871 -0.9023781 -0.6506600 -0.4522194
## hsa-mir-369 hsa-mir-370 hsa-mir-376a-1 hsa-mir-376a-2 hsa-mir-376b
## -0.5855907 -0.6299468 -0.6462057 -0.7213440 -0.6056218
## hsa-mir-376c hsa-mir-377 hsa-mir-379 hsa-mir-380 hsa-mir-381
## -0.5984895 -0.6137607 -0.5998633 -0.7333177 -0.5946947
## hsa-mir-382 hsa-mir-409 hsa-mir-410 hsa-mir-411 hsa-mir-412
## -0.6338445 -0.6219059 -0.6434716 -0.6958073 -0.5501088
## hsa-mir-431 hsa-mir-432 hsa-mir-433 hsa-mir-466 hsa-mir-485
## -0.6248299 -0.6426433 -0.6436876 0.4015545 -0.6906152
## hsa-mir-487a hsa-mir-487b hsa-mir-493 hsa-mir-494 hsa-mir-495
## -0.7452065 -0.6615326 -0.5307040 -0.6393844 -0.5588490
## hsa-mir-496 hsa-mir-539 hsa-mir-541 hsa-mir-543 hsa-mir-544
## -0.6347435 -0.6248115 -0.6876863 -0.6419155 -0.4143495
## hsa-mir-654 hsa-mir-655 hsa-mir-656 hsa-mir-665 hsa-mir-668
## -0.5842991 -0.7051487 -0.7722097 -0.6770739 -0.8606763
## hsa-mir-758 hsa-mir-770 hsa-mir-889
## -0.5809780 -0.7888620 -0.6473752
##
##
## $`2f`
## $`2f`$Factor1
## hsa-mir-1258 hsa-mir-135b hsa-mir-506 hsa-mir-508 hsa-mir-509-3
## -0.2733195 0.2678525 -0.3185482 -0.2774065 -0.2687342
## hsa-mir-510 hsa-mir-513a-1 hsa-mir-513a-2 hsa-mir-513b hsa-mir-513c
## -0.3650144 -0.3297462 -0.3227300 -0.3234853 -0.2877525
## hsa-mir-514-1 hsa-mir-514-2 hsa-mir-514-3 CTNNA1.R2Gn G6PD.RPPA
## -0.3280582 -0.3258505 -0.3244563 -0.2694667 -0.4501249
## IGFBP2.RPPA RBM15.RPPA ATM.RPPA FASN.RPPA INPP4B.RPPA
## 0.3018783 0.7999696 0.3250985 1.0536463 -0.4189671
## TSC1.RPPA TTF1.RPPA VHL.RPPA PRDX1.RPPA XBP1.RPPA
## 0.4269544 -0.3765308 -0.5905985 -0.5384414 -0.3626753
## MSH6.RPPA TFRC.RPPA MSH2.RPPA PREX1.RPPA
## 0.7180545 0.4532162 0.2702868 -0.4629907
##
## $`2f`$Factor2
## hsa-mir-1185-1 hsa-mir-1185-2 hsa-mir-1193 hsa-mir-1197 hsa-mir-127
## -0.8148004 -0.7998948 -0.6412522 -0.8151468 -0.6292322
## hsa-mir-134 hsa-mir-136 hsa-mir-137 hsa-mir-138-1 hsa-mir-154
## -0.5866563 -0.6456195 0.3196321 0.2904333 -0.6491630
## hsa-mir-299 hsa-mir-323 hsa-mir-323b hsa-mir-329-1 hsa-mir-329-2
## -0.6144646 -0.7357216 -0.7650560 -0.9230492 -0.6390089
## hsa-mir-337 hsa-mir-369 hsa-mir-370 hsa-mir-376a-1 hsa-mir-376a-2
## -0.4441141 -0.5933784 -0.6397646 -0.6545057 -0.7125216
## hsa-mir-376b hsa-mir-376c hsa-mir-377 hsa-mir-379 hsa-mir-380
## -0.6112866 -0.6071882 -0.6177324 -0.6089270 -0.7394387
## hsa-mir-381 hsa-mir-382 hsa-mir-409 hsa-mir-410 hsa-mir-411
## -0.6096473 -0.6500180 -0.6377656 -0.6699741 -0.7572727
## hsa-mir-412 hsa-mir-431 hsa-mir-432 hsa-mir-433 hsa-mir-466
## -0.5592501 -0.6241728 -0.6549299 -0.6954934 0.3784283
## hsa-mir-485 hsa-mir-487a hsa-mir-487b hsa-mir-493 hsa-mir-494
## -0.7505666 -0.7678460 -0.6853095 -0.5395591 -0.6570549
## hsa-mir-495 hsa-mir-496 hsa-mir-539 hsa-mir-541 hsa-mir-543
## -0.5905014 -0.6631960 -0.6498181 -0.6976724 -0.7016385
## hsa-mir-544 hsa-mir-577 hsa-mir-585 hsa-mir-654 hsa-mir-655
## -0.4388437 0.2662390 0.2703556 -0.5988272 -0.7417666
## hsa-mir-656 hsa-mir-665 hsa-mir-668 hsa-mir-758 hsa-mir-770
## -0.7694766 -0.6560661 -0.9011633 -0.5863475 -0.7715128
## hsa-mir-889
## -0.6736458
##
##
## $`3f`
## $`3f`$Factor1
## hsa-mir-1185-1 hsa-mir-1185-2 hsa-mir-1193 hsa-mir-1197 hsa-mir-1258
## -0.7649038 -0.7472290 -0.6257883 -0.8151400 0.3117462
## hsa-mir-127 hsa-mir-134 hsa-mir-136 hsa-mir-137 hsa-mir-138-1
## -0.6123154 -0.5905554 -0.6246587 0.3602757 0.2837456
## hsa-mir-154 hsa-mir-299 hsa-mir-323 hsa-mir-323b hsa-mir-329-1
## -0.6272125 -0.6030781 -0.7104303 -0.7207944 -0.9035395
## hsa-mir-329-2 hsa-mir-337 hsa-mir-369 hsa-mir-370 hsa-mir-376a-1
## -0.6551830 -0.4531594 -0.5869315 -0.6311082 -0.6467226
## hsa-mir-376a-2 hsa-mir-376b hsa-mir-376c hsa-mir-377 hsa-mir-379
## -0.7206759 -0.6064602 -0.5995535 -0.6144270 -0.6010460
## hsa-mir-380 hsa-mir-381 hsa-mir-382 hsa-mir-409 hsa-mir-410
## -0.7321005 -0.5965367 -0.6356706 -0.6233494 -0.6455569
## hsa-mir-411 hsa-mir-412 hsa-mir-431 hsa-mir-432 hsa-mir-433
## -0.7016670 -0.5505418 -0.6259743 -0.6441280 -0.6460453
## hsa-mir-466 hsa-mir-485 hsa-mir-487a hsa-mir-487b hsa-mir-489
## 0.4156560 -0.6992923 -0.7463014 -0.6639803 0.2486635
## hsa-mir-490 hsa-mir-493 hsa-mir-494 hsa-mir-495 hsa-mir-496
## 0.2658478 -0.5316300 -0.6413019 -0.5615859 -0.6368647
## hsa-mir-506 hsa-mir-507 hsa-mir-510 hsa-mir-513a-1 hsa-mir-513a-2
## 0.2518729 0.2209553 0.3320070 0.2278679 0.2806987
## hsa-mir-513b hsa-mir-513c hsa-mir-514-1 hsa-mir-514-2 hsa-mir-514-3
## 0.2429859 0.2522876 0.2285119 0.2285385 0.2270829
## hsa-mir-517a hsa-mir-539 hsa-mir-541 hsa-mir-543 hsa-mir-544
## 0.2227962 -0.6271768 -0.6866341 -0.6493149 -0.4138828
## hsa-mir-577 hsa-mir-585 hsa-mir-605 hsa-mir-653 hsa-mir-654
## 0.2761759 0.2673895 0.2718495 0.2246087 -0.5858963
## hsa-mir-655 hsa-mir-656 hsa-mir-665 hsa-mir-668 hsa-mir-758
## -0.7073773 -0.7716958 -0.6887911 -0.8602373 -0.5819465
## hsa-mir-770 hsa-mir-889 G6PD.RPPA FASN.RPPA INPP4B.RPPA
## -0.7952202 -0.6500319 0.2404191 -0.2885815 0.2408990
## PRDX1.RPPA
## 0.2636502
##
## $`3f`$Factor2
## hsa-mir-1226 hsa-mir-1258 hsa-mir-135b hsa-mir-139 hsa-mir-182
## 0.2233851 -0.4302970 0.2926786 0.3497486 0.2766422
## hsa-mir-183 hsa-mir-184 hsa-mir-187 hsa-mir-196a-1 hsa-mir-196a-2
## 0.2841530 -0.2375634 0.2371328 0.2896094 0.2599002
## hsa-mir-196b hsa-mir-2114 hsa-mir-218-1 hsa-mir-218-2 hsa-mir-3166
## 0.2862292 -0.3140284 0.2630450 0.3165759 0.3280705
## hsa-mir-3170 hsa-mir-3655 hsa-mir-383 hsa-mir-3917 hsa-mir-3923
## 0.2912757 -0.3138855 0.2283583 0.2294467 0.2732425
## hsa-mir-411 hsa-mir-485 hsa-mir-506 hsa-mir-507 hsa-mir-508
## -0.2500918 -0.2914957 -0.8235410 -0.8798237 -0.7841521
## hsa-mir-509-1 hsa-mir-509-2 hsa-mir-509-3 hsa-mir-510 hsa-mir-513a-1
## -0.7517999 -0.7475504 -0.7555578 -0.9424875 -0.8275008
## hsa-mir-513a-2 hsa-mir-513b hsa-mir-513c hsa-mir-514-1 hsa-mir-514-2
## -0.9246400 -0.7336730 -0.7541221 -0.8465889 -0.8511083
## hsa-mir-514-3 hsa-mir-514b hsa-mir-543 hsa-mir-615 hsa-mir-887
## -0.8518621 -0.7302340 -0.2690902 0.2833678 0.2814917
## hsa-mir-92b hsa-mir-96 RBM15.RPPA PTEN.RPPA TSC1.RPPA
## 0.2259010 0.2418153 0.3592209 0.2233962 0.3981680
## TTF1.RPPA VHL.RPPA PREX1.RPPA
## -0.2463980 -0.4164379 -0.2251980
##
## $`3f`$Factor3
## named numeric(0)
##
##
## $`5f`
## $`5f`$Factor1
## STMN1.R2Gn CDK1.R2Gn CCNB1.R2Gn G6PD.RPPA IGFBP2.RPPA RBM15.RPPA
## 0.1986635 0.2107954 0.1914999 -0.2784869 0.2231534 0.5884744
## GATA3.RPPA ATM.RPPA BRCA2.RPPA FASN.RPPA INPP4B.RPPA TSC1.RPPA
## -0.3249034 0.2610943 -0.2230770 0.9309107 -0.3657546 0.2800193
## TTF1.RPPA CDK1.RPPA VHL.RPPA PRDX1.RPPA XBP1.RPPA GAPDH.RPPA
## -0.2885557 -0.2259187 -0.4192049 -0.4660874 -0.3349707 0.3190805
## MSH6.RPPA MYH11.RPPA TFRC.RPPA MSH2.RPPA PREX1.RPPA
## 0.6825490 -0.2656290 0.4747938 0.2681282 -0.3944828
##
## $`5f`$Factor2
## hsa-mir-1185-1 hsa-mir-1185-2 hsa-mir-1193 hsa-mir-1197 hsa-mir-1258
## -0.7585875 -0.7579153 -0.6106161 -0.8063115 0.3553090
## hsa-mir-127 hsa-mir-129-2 hsa-mir-1291 hsa-mir-134 hsa-mir-135a-1
## -0.6067963 0.1967504 0.1958421 -0.5614834 0.2031226
## hsa-mir-136 hsa-mir-137 hsa-mir-138-1 hsa-mir-154 hsa-mir-205
## -0.6274709 0.3337672 0.2560318 -0.6174549 0.2176485
## hsa-mir-299 hsa-mir-323 hsa-mir-323b hsa-mir-329-1 hsa-mir-329-2
## -0.5925601 -0.7101262 -0.7288977 -0.9205374 -0.6773367
## hsa-mir-337 hsa-mir-33b hsa-mir-369 hsa-mir-370 hsa-mir-376a-1
## -0.4617565 0.1884892 -0.5758965 -0.6270633 -0.6579611
## hsa-mir-376a-2 hsa-mir-376b hsa-mir-376c hsa-mir-377 hsa-mir-379
## -0.6664014 -0.5960246 -0.5905546 -0.6045995 -0.5757390
## hsa-mir-380 hsa-mir-381 hsa-mir-382 hsa-mir-383 hsa-mir-3909
## -0.7120968 -0.5708246 -0.6251879 -0.1941954 0.1866493
## hsa-mir-3922 hsa-mir-409 hsa-mir-410 hsa-mir-411 hsa-mir-412
## 0.1996993 -0.6185533 -0.6469681 -0.6913067 -0.5558614
## hsa-mir-431 hsa-mir-432 hsa-mir-433 hsa-mir-466 hsa-mir-485
## -0.6398707 -0.6475080 -0.6672985 0.4424094 -0.6710682
## hsa-mir-487a hsa-mir-487b hsa-mir-488 hsa-mir-489 hsa-mir-490
## -0.7257411 -0.6719176 0.1999765 0.2445012 0.2758687
## hsa-mir-493 hsa-mir-494 hsa-mir-495 hsa-mir-496 hsa-mir-499
## -0.5388712 -0.6089900 -0.5462614 -0.6448792 0.2226947
## hsa-mir-506 hsa-mir-507 hsa-mir-508 hsa-mir-509-1 hsa-mir-509-2
## 0.3840058 0.3750684 0.3639676 0.3490401 0.3463436
## hsa-mir-509-3 hsa-mir-510 hsa-mir-513a-1 hsa-mir-513a-2 hsa-mir-513b
## 0.3466478 0.4551782 0.3447721 0.4144709 0.3474466
## hsa-mir-513c hsa-mir-514-1 hsa-mir-514-2 hsa-mir-514-3 hsa-mir-514b
## 0.3822525 0.3548202 0.3572057 0.3565667 0.3278773
## hsa-mir-517a hsa-mir-518f hsa-mir-520a hsa-mir-526b hsa-mir-539
## 0.2582380 0.1856824 0.2191678 0.1998557 -0.6358414
## hsa-mir-541 hsa-mir-543 hsa-mir-544 hsa-mir-577 hsa-mir-585
## -0.6879424 -0.6286093 -0.3783225 0.2676026 0.2643647
## hsa-mir-605 hsa-mir-654 hsa-mir-655 hsa-mir-656 hsa-mir-665
## 0.2569081 -0.5912489 -0.6985868 -0.7680615 -0.7129604
## hsa-mir-668 hsa-mir-758 hsa-mir-770 hsa-mir-889 hsa-mir-891a
## -0.8759764 -0.5601472 -0.8024955 -0.6434183 0.1956581
##
## $`5f`$Factor3
## hsa-mir-1185-1 hsa-mir-1185-2 hsa-mir-1197 hsa-mir-1226 hsa-mir-124-3
## -0.2693898 -0.2153963 -0.1982752 0.2103746 0.2058201
## hsa-mir-1249 hsa-mir-1255a hsa-mir-1258 hsa-mir-135b hsa-mir-139
## 0.2124197 0.1936285 -0.3686553 0.2490502 0.3217925
## hsa-mir-182 hsa-mir-183 hsa-mir-184 hsa-mir-187 hsa-mir-196a-1
## 0.2398068 0.2430847 -0.2246937 0.2105549 0.2294495
## hsa-mir-196a-2 hsa-mir-196b hsa-mir-206 hsa-mir-2114 hsa-mir-218-1
## 0.2111500 0.2401641 0.1875115 -0.2789480 0.2197055
## hsa-mir-218-2 hsa-mir-3166 hsa-mir-3170 hsa-mir-323 hsa-mir-323b
## 0.2598653 0.2902097 0.2486504 -0.1916817 -0.2305173
## hsa-mir-338 hsa-mir-3655 hsa-mir-376a-2 hsa-mir-379 hsa-mir-380
## 0.1898335 -0.2836783 -0.2643668 -0.1870428 -0.1919658
## hsa-mir-381 hsa-mir-383 hsa-mir-3917 hsa-mir-3923 hsa-mir-410
## -0.1987551 0.1977353 0.2001151 0.2339307 -0.1858580
## hsa-mir-411 hsa-mir-433 hsa-mir-485 hsa-mir-487a hsa-mir-494
## -0.2921805 -0.2019031 -0.3417393 -0.2342592 -0.2366182
## hsa-mir-495 hsa-mir-506 hsa-mir-507 hsa-mir-508 hsa-mir-509-1
## -0.1956948 -0.7359853 -0.8076562 -0.7308223 -0.7148668
## hsa-mir-509-2 hsa-mir-509-3 hsa-mir-510 hsa-mir-513a-1 hsa-mir-513a-2
## -0.7105480 -0.7097014 -0.8157004 -0.7257079 -0.8095509
## hsa-mir-513b hsa-mir-513c hsa-mir-514-1 hsa-mir-514-2 hsa-mir-514-3
## -0.6391351 -0.6802698 -0.7502505 -0.7560365 -0.7577167
## hsa-mir-514b hsa-mir-543 hsa-mir-544 hsa-mir-582 hsa-mir-615
## -0.6915826 -0.3114163 -0.2319221 0.2220790 0.2358871
## hsa-mir-655 hsa-mir-668 hsa-mir-887 hsa-mir-889 hsa-mir-92b
## -0.2241513 -0.2524937 0.2244516 -0.1886266 0.2053577
## hsa-mir-96
## 0.2137223
##
## $`5f`$Factor4
## PEA15.RPPA
## 0.1940685
##
## $`5f`$Factor5
## PARP1.R2Gn
## 0.1860451
##
##
## $`10f`
## $`10f`$Factor1
## hsa-mir-101-2 hsa-mir-1258 hsa-mir-139 hsa-mir-146a hsa-mir-150
## 0.1629177 0.1454717 -0.1527660 0.2439511 0.2176340
## hsa-mir-196a-1 hsa-mir-196a-2 hsa-mir-210 hsa-mir-218-2 hsa-mir-301b
## -0.1894599 -0.1409968 -0.1544269 -0.1662055 -0.1581296
## hsa-mir-3065 hsa-mir-362 hsa-mir-378c hsa-mir-3940 hsa-mir-488
## -0.1475613 0.2013512 0.1418129 -0.1491676 -0.1499323
## hsa-mir-510 hsa-mir-605 hsa-mir-653 hsa-mir-887 hsa-mir-9-1
## 0.1519868 0.1691677 0.2167146 -0.1459726 -0.1492127
## hsa-mir-9-2 hsa-mir-95 hsa-mir-99a CDH2.R2Gn FASN.R2Gn
## -0.1498007 -0.1506946 0.1655920 -0.1476591 -0.1960203
## PRKCA.R2Gn ANLN.R2Gn STMN1.R2Gn RAB11A.R2Gn ETS1.R2Gn
## 0.1897229 -0.1483475 -0.2373242 -0.1625782 0.1555535
## CDK1.R2Gn CTNNA1.R2Gn TYMS.R2Gn MSH6.R2Gn CCNB1.R2Gn
## -0.2289052 0.2068288 -0.1729913 -0.1780294 -0.2314913
## PDK1.R2Gn FOXM1.R2Gn COL6A1.R2Gn STAT5A.R2Gn YWHAB.R2Gn
## -0.1450866 -0.1603136 0.1483476 0.1690133 0.1658905
## ANXA1.R2Gn PREX1.R2Gn SQSTM1.R2Gn G6PD.RPPA IGFBP2.RPPA
## 0.1529496 0.1735357 0.1430024 0.4649610 -0.2495660
## ASNS.RPPA RBM15.RPPA GATA3.RPPA PEA15.RPPA ATM.RPPA
## 0.1845150 -0.7031606 0.4185162 -0.1961371 -0.2976696
## BRCA2.RPPA FASN.RPPA INPP4B.RPPA ACVRL1.RPPA TSC1.RPPA
## 0.2778099 -1.1854465 0.4445420 0.1634472 -0.3088216
## TTF1.RPPA CDK1.RPPA VHL.RPPA AR.RPPA PRDX1.RPPA
## 0.3018635 0.3171725 0.5434133 0.1688745 0.5653009
## XBP1.RPPA GAPDH.RPPA MSH6.RPPA MYH11.RPPA PDK1.RPPA
## 0.3994834 -0.5204806 -0.8080000 0.2798145 0.1510109
## TFRC.RPPA MSH2.RPPA PREX1.RPPA
## -0.4650862 -0.2984680 0.5079902
##
## $`10f`$Factor2
## hsa-mir-100 hsa-mir-105-2 hsa-mir-1185-1 hsa-mir-1185-2 hsa-mir-1193
## 0.1667214 0.1476208 -0.7757787 -0.7684686 -0.6118972
## hsa-mir-1197 hsa-mir-1224 hsa-mir-1245 hsa-mir-1247 hsa-mir-1251
## -0.8106640 0.1649559 0.1708265 0.1578687 0.1508070
## hsa-mir-1258 hsa-mir-127 hsa-mir-1270-2 hsa-mir-129-2 hsa-mir-1291
## 0.2967204 -0.6143032 -0.1482040 0.2151572 0.1911404
## hsa-mir-134 hsa-mir-135a-1 hsa-mir-136 hsa-mir-137 hsa-mir-138-1
## -0.5639862 0.2104407 -0.6320459 0.3159860 0.2708478
## hsa-mir-138-2 hsa-mir-154 hsa-mir-1909 hsa-mir-204 hsa-mir-205
## 0.1934429 -0.6310229 -0.1482276 0.1670878 0.2006872
## hsa-mir-206 hsa-mir-2114 hsa-mir-299 hsa-mir-3193 hsa-mir-323
## 0.1796628 0.1568462 -0.6040230 0.1416263 -0.7222756
## hsa-mir-323b hsa-mir-329-1 hsa-mir-329-2 hsa-mir-337 hsa-mir-33b
## -0.7419769 -0.9263064 -0.6799496 -0.4582561 0.1917758
## hsa-mir-34b hsa-mir-369 hsa-mir-370 hsa-mir-376a-1 hsa-mir-376a-2
## 0.1495366 -0.5849407 -0.6314871 -0.6638160 -0.6738463
## hsa-mir-376b hsa-mir-376c hsa-mir-377 hsa-mir-379 hsa-mir-380
## -0.6039874 -0.5940351 -0.6003941 -0.5850655 -0.7232468
## hsa-mir-381 hsa-mir-382 hsa-mir-383 hsa-mir-3909 hsa-mir-3922
## -0.5862670 -0.6325155 -0.1731483 0.1873861 0.1956569
## hsa-mir-3934 hsa-mir-409 hsa-mir-410 hsa-mir-411 hsa-mir-412
## 0.1405914 -0.6230285 -0.6622328 -0.7261397 -0.5606990
## hsa-mir-431 hsa-mir-432 hsa-mir-433 hsa-mir-466 hsa-mir-485
## -0.6425268 -0.6511705 -0.6874613 0.4145631 -0.6997358
## hsa-mir-487a hsa-mir-487b hsa-mir-488 hsa-mir-489 hsa-mir-490
## -0.7420009 -0.6732689 0.2419606 0.2291096 0.2628658
## hsa-mir-493 hsa-mir-494 hsa-mir-495 hsa-mir-496 hsa-mir-499
## -0.5468529 -0.6323493 -0.5617642 -0.6429590 0.2313994
## hsa-mir-506 hsa-mir-507 hsa-mir-508 hsa-mir-509-1 hsa-mir-509-2
## 0.3096959 0.3055074 0.2930038 0.2866548 0.2849193
## hsa-mir-509-3 hsa-mir-510 hsa-mir-513a-1 hsa-mir-513a-2 hsa-mir-513b
## 0.2869746 0.3737925 0.2657331 0.3251164 0.2889396
## hsa-mir-513c hsa-mir-514-1 hsa-mir-514-2 hsa-mir-514-3 hsa-mir-514b
## 0.3184157 0.2776071 0.2795785 0.2788993 0.2689486
## hsa-mir-517a hsa-mir-518b hsa-mir-518f hsa-mir-520a hsa-mir-526b
## 0.2644774 0.1626558 0.1716351 0.2239893 0.2047622
## hsa-mir-539 hsa-mir-541 hsa-mir-543 hsa-mir-544 hsa-mir-548s
## -0.6406990 -0.6928630 -0.6504994 -0.3885738 0.1430110
## hsa-mir-548v hsa-mir-550a-2 hsa-mir-577 hsa-mir-585 hsa-mir-605
## 0.1809890 0.1542264 0.2681238 0.2737091 0.2267991
## hsa-mir-639 hsa-mir-653 hsa-mir-654 hsa-mir-655 hsa-mir-656
## 0.1789042 0.1557767 -0.5932516 -0.7303706 -0.7603929
## hsa-mir-665 hsa-mir-668 hsa-mir-676 hsa-mir-758 hsa-mir-767
## -0.6939368 -0.8925683 0.1587216 -0.5663007 0.1807970
## hsa-mir-770 hsa-mir-889 hsa-mir-891a hsa-mir-95
## -0.7861210 -0.6554383 0.1917885 0.1398462
##
## $`10f`$Factor3
## G6PD.RPPA IGFBP2.RPPA RBM15.RPPA PTEN.RPPA GATA3.RPPA PEA15.RPPA
## 0.3529247 0.2235950 -0.3091065 -0.4563414 0.1400799 -0.2244356
## ATM.RPPA EGFR.RPPA INPP4B.RPPA ACVRL1.RPPA TSC1.RPPA PDCD4.RPPA
## -0.2509778 -0.1518510 0.2045552 0.1401543 -0.1826618 -0.4109748
## CDK1.RPPA VHL.RPPA PRDX1.RPPA XBP1.RPPA ERCC1.RPPA TFRC.RPPA
## 0.1680966 0.2265389 0.2595026 0.2400194 -0.1476577 -0.1788825
## PREX1.RPPA
## 0.2135643
##
## $`10f`$Factor4
## hsa-mir-1185-1 hsa-mir-1185-2 hsa-mir-1197 hsa-mir-1224 hsa-mir-1226
## -0.1899032 -0.1406181 -0.1567997 -0.1622436 0.2013880
## hsa-mir-1229 hsa-mir-124-3 hsa-mir-1249 hsa-mir-1255a hsa-mir-1258
## 0.1627852 0.1972792 0.2013092 0.1628381 -0.3447852
## hsa-mir-1291 hsa-mir-1292 hsa-mir-135b hsa-mir-139 hsa-mir-182
## -0.1428185 0.1776674 0.2185706 0.2925311 0.2095041
## hsa-mir-183 hsa-mir-184 hsa-mir-187 hsa-mir-196a-1 hsa-mir-196a-2
## 0.2128228 -0.2045339 0.1699140 0.1975691 0.1904193
## hsa-mir-196b hsa-mir-206 hsa-mir-210 hsa-mir-2114 hsa-mir-216b
## 0.2097269 0.1561514 -0.1582593 -0.2516953 -0.1971690
## hsa-mir-218-1 hsa-mir-218-2 hsa-mir-3166 hsa-mir-3170 hsa-mir-3190
## 0.1833000 0.2043498 0.2622004 0.2178932 0.1418359
## hsa-mir-3199-1 hsa-mir-323b hsa-mir-338 hsa-mir-3605 hsa-mir-3655
## -0.1625380 -0.1555429 0.1969098 0.1488437 -0.2656059
## hsa-mir-3690 hsa-mir-376a-2 hsa-mir-383 hsa-mir-3917 hsa-mir-3923
## -0.1430867 -0.2118430 0.1994986 0.1702260 0.2342099
## hsa-mir-3926-2 hsa-mir-411 hsa-mir-466 hsa-mir-485 hsa-mir-487a
## -0.1606206 -0.1949755 -0.1413170 -0.2529788 -0.1521015
## hsa-mir-494 hsa-mir-506 hsa-mir-507 hsa-mir-508 hsa-mir-509-1
## -0.1615179 -0.6782678 -0.7587051 -0.6876708 -0.6887159
## hsa-mir-509-2 hsa-mir-509-3 hsa-mir-510 hsa-mir-511-2 hsa-mir-513a-1
## -0.6844518 -0.6827294 -0.8044964 -0.1585291 -0.6867524
## hsa-mir-513a-2 hsa-mir-513b hsa-mir-513c hsa-mir-514-1 hsa-mir-514-2
## -0.7446260 -0.6228126 -0.6547784 -0.6779802 -0.6837980
## hsa-mir-514-3 hsa-mir-514b hsa-mir-543 hsa-mir-544 hsa-mir-582
## -0.6835320 -0.6983735 -0.2354951 -0.1853546 0.2105771
## hsa-mir-615 hsa-mir-668 hsa-mir-760 hsa-mir-876 hsa-mir-887
## 0.2115752 -0.1888667 0.1482735 -0.1476502 0.1912648
## hsa-mir-92b hsa-mir-96
## 0.2082682 0.1794035
##
## $`10f`$Factor5
## IGFBP2.RPPA RBM15.RPPA EGFR.RPPA TSC1.RPPA GAPDH.RPPA ERCC1.RPPA
## 0.1432934 0.1444952 -0.1754455 0.1546405 -0.1664315 -0.1930599
##
## $`10f`$Factor6
## G6PD.RPPA ASNS.RPPA RBM15.RPPA GATA3.RPPA EGFR.RPPA GAPDH.RPPA PREX1.RPPA
## 0.1433544 0.1942848 -0.2828889 -0.1858416 0.1668751 0.1652671 -0.2089479
##
## $`10f`$Factor7
## ANLN.R2Gn STMN1.R2Gn CDK1.R2Gn CCNB1.R2Gn FOXM1.R2Gn
## 0.2266988 0.2299727 0.2035736 0.2148030 0.1838917
##
## $`10f`$Factor8
## named numeric(0)
##
## $`10f`$Factor9
## named numeric(0)
##
## $`10f`$Factor10
## named numeric(0)1. Convert microRNA to genes
Also remove the ending “.R2Gn” and “.RPPA” from gene names.
split.by.omic = function(variable.list) {
out.mRSG = variable.list[startsWith(variable.list, "hsa")]
out.R2Gn = variable.list[endsWith(variable.list, ".R2Gn")]
out.RPPA = variable.list[endsWith(variable.list, ".RPPA")]
out = list("miRNASeqGene" = out.mRSG,
"RNASeq2GeneNorm" = out.R2Gn,
"RPPAArray" = out.RPPA)
out
}multiomics.to.GENES = function(sel.features, full.search = F, table = "validated", drop.miRNA = F) {
multiomics.list = split.by.omic(sel.features)
# Convert miRNASeqGene to target GENE names
# Skipped and returns an empty list instead of the list of select features,
# or if microRNA features are explicitly dropped (drop.miRNA = T).
# (Usually done when the features has only a few miRNA and unable to target any genes)
if (length(multiomics.list[[1]]) > 0 & !drop.miRNA) {
if (!full.search) { # Search only among the 198 genes in ACC, recommended
targets= get_multimir(mirna = multiomics.list[[1]],
target = gene.names,
table = table,
summary = T)
mRSG.target.genes = unique(targets@data$target_symbol)
} else { # Search the full dataset, not recommended.
# Use only if ACC gene search returns nothing or fails.
# Genes not in the ACC genes need to be manually removed.
targets= get_multimir(mirna = multiomics.list[[1]],
table = table,
summary = T)
mRSG.target.genes = unique(targets@data$target_symbol)
}
} else {
mRSG.target.genes = list()
}
#Remove suffix for Pathway Analysis Compatibility
R2Gn.genes = str_remove(multiomics.list[[2]], ".R2Gn")
RPPA.genes = str_remove(multiomics.list[[3]], ".RPPA")
#Join all cleaned-up genes are remove duplicates.
out1 = c(mRSG.target.genes, R2Gn.genes, RPPA.genes)
out = as.character(unique(out1))
out
}geneNames <- list("Factor1of1"= multiomics.to.GENES(names(sel.features$`1f`$Factor1)),
"Factor1of2"= multiomics.to.GENES(names(sel.features$`2f`$Factor1)),
"Factor2of2"= multiomics.to.GENES(names(sel.features$`2f`$Factor2)),
"Factor1of3"= multiomics.to.GENES(names(sel.features$`3f`$Factor1)),
"Factor2of3"= multiomics.to.GENES(names(sel.features$`3f`$Factor2)),
"Factor3of3"= multiomics.to.GENES(names(sel.features$`3f`$Factor3)), # Empty
"Factor1of5"= multiomics.to.GENES(names(sel.features$`5f`$Factor1)),
"Factor2of5"= multiomics.to.GENES(names(sel.features$`5f`$Factor2)),
"Factor3of5"= multiomics.to.GENES(names(sel.features$`5f`$Factor3)),
"Factor4of5"= multiomics.to.GENES(names(sel.features$`5f`$Factor4)),
"Factor5of5"= multiomics.to.GENES(names(sel.features$`5f`$Factor5)),
"Factor1of10"= multiomics.to.GENES(names(sel.features$`10f`$Factor1)),
"Factor2of10"= multiomics.to.GENES(names(sel.features$`10f`$Factor2)),
"Factor3of10"= multiomics.to.GENES(names(sel.features$`10f`$Factor3)),
"Factor4of10"= multiomics.to.GENES(names(sel.features$`10f`$Factor4)),
"Factor5of10"= multiomics.to.GENES(names(sel.features$`10f`$Factor5)),
"Factor6of10"= multiomics.to.GENES(names(sel.features$`10f`$Factor6)),
"Factor7of10"= multiomics.to.GENES(names(sel.features$`10f`$Factor7)),
"Factor8of10"= multiomics.to.GENES(names(sel.features$`10f`$Factor8)), # Empty
"Factor9of10"= multiomics.to.GENES(names(sel.features$`10f`$Factor9)), # Empty
"Factor10of10"= multiomics.to.GENES(names(sel.features$`10f`$Factor10)) # Empty
)## Searching mirecords ...
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## Searching tarbase ...geneNames## $Factor1of1
## [1] "HSPA1A" "AKT1" "VHL" "MTOR" "MAPK8" "MYH9" "CDKN1A"
## [8] "FOXO3" "ATM" "CASP8" "MACC1" "PTEN" "KRAS" "NRAS"
## [15] "PTK2" "ETS1" "CCND1" "PIK3R1" "XIAP" "CHEK1" "IGF1R"
## [22] "SRSF1" "TUBA1B" "STAT5A" "KIT" "NCOA3" "EGFR" "EZH2"
## [29] "PTGS2" "MET" "AKT2" "YBX1" "PRKAA1" "PXN" "AXL"
## [36] "MSH2" "CASP3" "CCNE1" "YAP1" "EIF4E" "EIF4G1" "GAPDH"
## [43] "ITGA2" "PRKCA" "MAPK1" "TFRC" "YWHAE" "RAB11A" "ANLN"
## [50] "RICTOR" "TP53BP1" "BRAF"
##
## $Factor1of2
## [1] "RB1" "XIAP" "CTNNA1" "G6PD" "IGFBP2" "RBM15" "ATM" "FASN"
## [9] "INPP4B" "TSC1" "TTF1" "VHL" "PRDX1" "XBP1" "MSH6" "TFRC"
## [17] "MSH2" "PREX1"
##
## $Factor2of2
## [1] "HSPA1A" "AKT1" "VHL" "MTOR" "MAPK8" "MYH9" "CDKN1A"
## [8] "FOXO3" "ATM" "CASP8" "MACC1" "PTEN" "KRAS" "NRAS"
## [15] "PTK2" "ETS1" "PARP1" "IGF1R" "CCNE2" "RAB25" "CCND1"
## [22] "PIK3R1" "XIAP" "CHEK1" "SRSF1" "TUBA1B" "STAT5A" "KIT"
## [29] "NCOA3" "EGFR" "EZH2" "PTGS2" "MET" "AKT2" "YBX1"
## [36] "PRKAA1" "PXN" "BCL2" "AXL" "MYC" "MSH2" "CASP3"
## [43] "BCL2L11" "CCNE1" "YAP1" "EIF4E" "EIF4G1" "GAPDH" "MSH6"
## [50] "ITGA2" "PIK3CA" "PRKCA" "MAPK1" "TFRC" "YWHAE" "RAB11A"
## [57] "ANLN" "RICTOR" "TP53BP1" "BRAF"
##
## $Factor1of3
## [1] "RB1" "XIAP" "HSPA1A" "AKT1" "VHL" "MTOR" "MAPK8"
## [8] "ETS1" "ARID1A" "BID" "MYH9" "CDKN1A" "FOXO3" "ATM"
## [15] "CASP8" "MACC1" "PTEN" "KRAS" "NRAS" "PTK2" "PARP1"
## [22] "IGF1R" "CCNE2" "RAB25" "CCND1" "PIK3R1" "CHEK1" "SRSF1"
## [29] "TUBA1B" "STAT5A" "KIT" "NCOA3" "EGFR" "EZH2" "PTGS2"
## [36] "MET" "AKT2" "YBX1" "PRKAA1" "PXN" "BCL2" "AXL"
## [43] "MYC" "MSH2" "CASP3" "BCL2L11" "CCNE1" "YAP1" "EIF4E"
## [50] "EIF4G1" "GAPDH" "MSH6" "ITGA2" "PIK3CA" "PRKCA" "MAPK1"
## [57] "TFRC" "YWHAE" "RAB11A" "GAB2" "ANLN" "RICTOR" "TP53BP1"
## [64] "BRAF" "G6PD" "FASN" "INPP4B" "PRDX1"
##
## $Factor2of3
## [1] "AKT2" "BCL2" "MYC" "AKT1" "BCL2L1" "RB1" "XIAP" "ETS1"
## [9] "MAPK8" "ARID1A" "BID" "PTEN" "KRAS" "NRAS" "PTK2" "ATM"
## [17] "YWHAZ" "CCND1" "CDKN1A" "NF2" "NCOA3" "ITGA2" "GAB2" "RBM15"
## [25] "TSC1" "TTF1" "VHL" "PREX1"
##
## $Factor3of3
## character(0)
##
## $Factor1of5
## [1] "STMN1" "CDK1" "CCNB1" "G6PD" "IGFBP2" "RBM15" "GATA3" "ATM"
## [9] "BRCA2" "FASN" "INPP4B" "TSC1" "TTF1" "VHL" "PRDX1" "XBP1"
## [17] "GAPDH" "MSH6" "MYH11" "TFRC" "MSH2" "PREX1"
##
## $Factor2of5
## [1] "RB1" "XIAP" "HSPA1A" "AKT1" "VHL" "MTOR" "MAPK8"
## [8] "ETS1" "ARID1A" "BID" "MYH9" "CDKN1A" "FOXO3" "ATM"
## [15] "CASP8" "MACC1" "PTEN" "KRAS" "NRAS" "PTK2" "PARP1"
## [22] "IGF1R" "CCNE2" "RAB25" "CCND1" "PIK3R1" "CHEK1" "SRSF1"
## [29] "TUBA1B" "STAT5A" "KIT" "NCOA3" "EGFR" "EZH2" "PTGS2"
## [36] "MET" "AKT2" "YBX1" "PRKAA1" "PXN" "BCL2" "E2F1"
## [43] "CASP9" "AXL" "CDKN2A" "MYC" "MSH2" "CASP3" "BCL2L11"
## [50] "CCNE1" "MAPK9" "RAF1" "YAP1" "BCL2L1" "DVL3" "EIF4E"
## [57] "EIF4G1" "GAPDH" "MSH6" "ITGA2" "SMAD3" "PIK3CA" "PRKCA"
## [64] "MAPK1" "MAPK3" "TFRC" "YWHAE" "RAB11A" "GAB2" "ANLN"
## [71] "RICTOR" "TP53BP1" "BRAF"
##
## $Factor3of5
## [1] "ESR1" "MET" "AKT2" "G6PD" "BCL2" "KRAS" "CCND1" "NOTCH3"
## [9] "AKT1" "IGF1R" "MYC" "BCL2L1" "RB1" "XIAP" "ETS1" "MAPK8"
## [17] "ARID1A" "BID" "PTEN" "NRAS" "PTK2" "ATM" "YWHAZ" "ITGA2"
## [25] "MAPK1" "PXN" "YWHAB" "CDKN1A" "STAT5A" "NF2" "NCOA3" "FOXO3"
## [33] "CHEK1" "FN1" "XRCC1" "GAB2"
##
## $Factor4of5
## [1] "PEA15"
##
## $Factor5of5
## [1] "PARP1"
##
## $Factor1of10
## [1] "RB1" "XIAP" "AKT1" "ACACA" "PTEN" "BCL2" "BCL2L11"
## [8] "PARP1" "CTNNA1" "EEF2" "GATA3" "NRG1" "IGF1R" "MAPK1"
## [15] "TFRC" "NDRG1" "AKT1S1" "RICTOR" "TP53BP1" "GSK3A" "CDH2"
## [22] "FASN" "PRKCA" "ANLN" "STMN1" "RAB11A" "ETS1" "CDK1"
## [29] "TYMS" "MSH6" "CCNB1" "PDK1" "FOXM1" "COL6A1" "STAT5A"
## [36] "YWHAB" "ANXA1" "PREX1" "SQSTM1" "G6PD" "IGFBP2" "ASNS"
## [43] "RBM15" "PEA15" "ATM" "BRCA2" "INPP4B" "ACVRL1" "TSC1"
## [50] "TTF1" "VHL" "AR" "PRDX1" "XBP1" "GAPDH" "MYH11"
## [57] "MSH2"
##
## $Factor2of10
## [1] "ESR1" "MET" "G6PD" "BCL2" "KRAS" "CCND1" "NOTCH3"
## [8] "AKT1" "IGF1R" "RB1" "XIAP" "CDKN1A" "HSPA1A" "VHL"
## [15] "MTOR" "MAPK8" "ETS1" "ARID1A" "BID" "MYH9" "FOXO3"
## [22] "ATM" "CASP8" "MACC1" "PTEN" "NRAS" "PTK2" "PARP1"
## [29] "CCNE2" "RAB25" "AR" "EIF4E" "MAPT" "RAD51" "ERCC1"
## [36] "PIK3R1" "CHEK1" "SRSF1" "TUBA1B" "STAT5A" "CDKN1B" "BCL2L11"
## [43] "KIT" "NCOA3" "EGFR" "EZH2" "PTGS2" "AKT2" "YBX1"
## [50] "PRKAA1" "PXN" "E2F1" "CASP9" "AXL" "CDKN2A" "MYC"
## [57] "MSH2" "CASP3" "CCNE1" "MAPK9" "RAF1" "YAP1" "BCL2L1"
## [64] "DVL3" "EIF4G1" "FN1" "GAPDH" "MSH6" "ITGA2" "SMAD3"
## [71] "SMAD4" "PIK3CA" "PRKCA" "MAPK1" "MAPK3" "TFRC" "YWHAE"
## [78] "RAB11A" "GAB2" "ANLN" "RICTOR" "TP53BP1" "BRAF"
##
## $Factor3of10
## [1] "G6PD" "IGFBP2" "RBM15" "PTEN" "GATA3" "PEA15" "ATM" "EGFR"
## [9] "INPP4B" "ACVRL1" "TSC1" "PDCD4" "CDK1" "VHL" "PRDX1" "XBP1"
## [17] "ERCC1" "TFRC" "PREX1"
##
## $Factor4of10
## [1] "ESR1" "MET" "AKT2" "G6PD" "BCL2" "KRAS" "CCND1" "NOTCH3"
## [9] "AKT1" "IGF1R" "MYC" "BCL2L1" "RB1" "XIAP" "TUBA1B" "ETS1"
## [17] "MAPK8" "ARID1A" "BID" "PTEN" "NRAS" "PTK2" "ATM" "YWHAZ"
## [25] "ITGA2" "MAPK1" "PXN" "YWHAB" "PIK3R1" "CHEK1" "SRSF1" "CDKN1A"
## [33] "STAT5A" "RAF1" "PRKAA1" "ACACA" "NF2" "NCOA3" "E2F1" "CASP9"
## [41] "AXL" "CDKN2A" "CCNE1" "MAPK9" "FOXO3" "CTNNB1" "DVL3" "FN1"
## [49] "SMAD3" "PRKCA" "MAPK3" "XRCC1" "GAB2" "WWTR1" "TSC2"
##
## $Factor5of10
## [1] "IGFBP2" "RBM15" "EGFR" "TSC1" "GAPDH" "ERCC1"
##
## $Factor6of10
## [1] "G6PD" "ASNS" "RBM15" "GATA3" "EGFR" "GAPDH" "PREX1"
##
## $Factor7of10
## [1] "ANLN" "STMN1" "CDK1" "CCNB1" "FOXM1"
##
## $Factor8of10
## character(0)
##
## $Factor9of10
## character(0)
##
## $Factor10of10
## character(0)saveRDS(geneNames, file = "data/sel_features/gene_converted/genes_mofa_extracted_by_bic.rds")2. Pathway Analysis
A. GO Classification
ggo_MF <- list()#functional profile of a geneset for Molecular Function
ggo_BP <- list()#functional profile of a geneset for Biological Process
ggo_CC <- list()#functional profile of a geneset for Cellular Component
for(z in 1:length(geneNames)){
print(z)
input <- geneNames[[z]]
ggo_MF[[z]] <- groupGO(gene=input,
OrgDb = org.Hs.eg.db,
ont="MF",
keyType="SYMBOL",
readable=TRUE)
ggo_BP[[z]] <- groupGO(gene=input,
OrgDb = org.Hs.eg.db,
ont="BP",
keyType="SYMBOL",
readable=TRUE)
ggo_CC[[z]] <- groupGO(gene=input,
OrgDb = org.Hs.eg.db,
ont="CC",
keyType="SYMBOL",
readable=TRUE)
}## [1] 1
## [1] 2
## [1] 3
## [1] 4
## [1] 5
## [1] 6
## [1] 7
## [1] 8
## [1] 9
## [1] 10
## [1] 11
## [1] 12
## [1] 13
## [1] 14
## [1] 15
## [1] 16
## [1] 17
## [1] 18
## [1] 19
## [1] 20
## [1] 21for(z in 1:length(geneNames)) {
print(head(ggo_MF[[z]]))
print(head(ggo_BP[[z]]))
print(head(ggo_CC[[z]]))
}## ID Description Count GeneRatio
## GO:0003774 GO:0003774 cytoskeletal motor activity 1 1/52
## GO:0003824 GO:0003824 catalytic activity 35 35/52
## GO:0005198 GO:0005198 structural molecule activity 1 1/52
## GO:0005215 GO:0005215 transporter activity 1 1/52
## GO:0005488 GO:0005488 binding 52 52/52
## GO:0009055 GO:0009055 electron transfer activity 0 0/52
## geneID
## GO:0003774 MYH9
## GO:0003824 HSPA1A/AKT1/VHL/MTOR/MAPK8/CDKN1A/ATM/CASP8/PTEN/KRAS/NRAS/PTK2/CCND1/PIK3R1/XIAP/CHEK1/IGF1R/TUBA1B/KIT/NCOA3/EGFR/EZH2/PTGS2/MET/AKT2/PRKAA1/AXL/MSH2/CASP3/CCNE1/GAPDH/PRKCA/MAPK1/RAB11A/BRAF
## GO:0005198 TUBA1B
## GO:0005215 IGF1R
## GO:0005488 HSPA1A/AKT1/VHL/MTOR/MAPK8/MYH9/CDKN1A/FOXO3/ATM/CASP8/MACC1/PTEN/KRAS/NRAS/PTK2/ETS1/CCND1/PIK3R1/XIAP/CHEK1/IGF1R/SRSF1/TUBA1B/STAT5A/KIT/NCOA3/EGFR/EZH2/PTGS2/MET/AKT2/YBX1/PRKAA1/PXN/AXL/MSH2/CASP3/CCNE1/YAP1/EIF4E/EIF4G1/GAPDH/ITGA2/PRKCA/MAPK1/TFRC/YWHAE/RAB11A/ANLN/RICTOR/TP53BP1/BRAF
## GO:0009055
## ID Description Count GeneRatio
## GO:0000003 GO:0000003 reproduction 16 16/52
## GO:0002376 GO:0002376 immune system process 27 27/52
## GO:0008152 GO:0008152 metabolic process 47 47/52
## GO:0009987 GO:0009987 cellular process 52 52/52
## GO:0016032 GO:0016032 viral process 6 6/52
## GO:0022414 GO:0022414 reproductive process 16 16/52
## geneID
## GO:0000003 AKT1/MTOR/MYH9/FOXO3/ATM/CASP8/PTEN/IGF1R/KIT/EGFR/PTGS2/AXL/MSH2/CASP3/CCNE1/ITGA2
## GO:0002376 HSPA1A/AKT1/MTOR/MAPK8/MYH9/CDKN1A/FOXO3/ATM/CASP8/PTK2/ETS1/PIK3R1/XIAP/IGF1R/KIT/EZH2/AXL/MSH2/CASP3/GAPDH/ITGA2/PRKCA/MAPK1/TFRC/YWHAE/TP53BP1/BRAF
## GO:0008152 HSPA1A/AKT1/VHL/MTOR/MAPK8/MYH9/CDKN1A/FOXO3/ATM/CASP8/MACC1/PTEN/KRAS/PTK2/ETS1/CCND1/PIK3R1/XIAP/CHEK1/IGF1R/SRSF1/STAT5A/KIT/NCOA3/EGFR/EZH2/PTGS2/MET/AKT2/YBX1/PRKAA1/AXL/MSH2/CASP3/CCNE1/YAP1/EIF4E/EIF4G1/GAPDH/ITGA2/PRKCA/MAPK1/TFRC/YWHAE/RICTOR/TP53BP1/BRAF
## GO:0009987 HSPA1A/AKT1/VHL/MTOR/MAPK8/MYH9/CDKN1A/FOXO3/ATM/CASP8/MACC1/PTEN/KRAS/NRAS/PTK2/ETS1/CCND1/PIK3R1/XIAP/CHEK1/IGF1R/SRSF1/TUBA1B/STAT5A/KIT/NCOA3/EGFR/EZH2/PTGS2/MET/AKT2/YBX1/PRKAA1/PXN/AXL/MSH2/CASP3/CCNE1/YAP1/EIF4E/EIF4G1/GAPDH/ITGA2/PRKCA/MAPK1/TFRC/YWHAE/RAB11A/ANLN/RICTOR/TP53BP1/BRAF
## GO:0016032 HSPA1A/AKT1/EGFR/AXL/ITGA2/TFRC
## GO:0022414 AKT1/MTOR/MYH9/FOXO3/ATM/CASP8/PTEN/IGF1R/KIT/EGFR/PTGS2/AXL/MSH2/CASP3/CCNE1/ITGA2
## ID Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex 38 38/52
## GO:0044423 GO:0044423 virion component 0 0/52
## GO:0110165 GO:0110165 cellular anatomical entity 52 52/52
## geneID
## GO:0032991 HSPA1A/AKT1/MTOR/MYH9/CDKN1A/FOXO3/ATM/CASP8/ETS1/CCND1/PIK3R1/CHEK1/IGF1R/SRSF1/STAT5A/KIT/NCOA3/EGFR/EZH2/PTGS2/MET/YBX1/PRKAA1/PXN/AXL/MSH2/CASP3/CCNE1/YAP1/EIF4E/EIF4G1/GAPDH/ITGA2/PRKCA/TFRC/RAB11A/RICTOR/TP53BP1
## GO:0044423
## GO:0110165 HSPA1A/AKT1/VHL/MTOR/MAPK8/MYH9/CDKN1A/FOXO3/ATM/CASP8/MACC1/PTEN/KRAS/NRAS/PTK2/ETS1/CCND1/PIK3R1/XIAP/CHEK1/IGF1R/SRSF1/TUBA1B/STAT5A/KIT/NCOA3/EGFR/EZH2/PTGS2/MET/AKT2/YBX1/PRKAA1/PXN/AXL/MSH2/CASP3/CCNE1/YAP1/EIF4E/EIF4G1/GAPDH/ITGA2/PRKCA/MAPK1/TFRC/YWHAE/RAB11A/ANLN/RICTOR/TP53BP1/BRAF
## ID Description Count GeneRatio
## GO:0003774 GO:0003774 cytoskeletal motor activity 0 0/18
## GO:0003824 GO:0003824 catalytic activity 9 9/18
## GO:0005198 GO:0005198 structural molecule activity 1 1/18
## GO:0005215 GO:0005215 transporter activity 0 0/18
## GO:0005488 GO:0005488 binding 18 18/18
## GO:0009055 GO:0009055 electron transfer activity 0 0/18
## geneID
## GO:0003774
## GO:0003824 XIAP/G6PD/ATM/FASN/INPP4B/VHL/PRDX1/MSH6/MSH2
## GO:0005198 CTNNA1
## GO:0005215
## GO:0005488 RB1/XIAP/CTNNA1/G6PD/IGFBP2/RBM15/ATM/FASN/INPP4B/TSC1/TTF1/VHL/PRDX1/XBP1/MSH6/TFRC/MSH2/PREX1
## GO:0009055
## ID Description Count GeneRatio
## GO:0000003 GO:0000003 reproduction 6 6/18
## GO:0002376 GO:0002376 immune system process 13 13/18
## GO:0008152 GO:0008152 metabolic process 16 16/18
## GO:0009987 GO:0009987 cellular process 18 18/18
## GO:0016032 GO:0016032 viral process 1 1/18
## GO:0022414 GO:0022414 reproductive process 6 6/18
## geneID
## GO:0000003 RB1/CTNNA1/IGFBP2/ATM/MSH6/MSH2
## GO:0002376 RB1/XIAP/G6PD/IGFBP2/RBM15/ATM/TSC1/PRDX1/XBP1/MSH6/TFRC/MSH2/PREX1
## GO:0008152 RB1/XIAP/G6PD/RBM15/ATM/FASN/INPP4B/TSC1/TTF1/VHL/PRDX1/XBP1/MSH6/TFRC/MSH2/PREX1
## GO:0009987 RB1/XIAP/CTNNA1/G6PD/IGFBP2/RBM15/ATM/FASN/INPP4B/TSC1/TTF1/VHL/PRDX1/XBP1/MSH6/TFRC/MSH2/PREX1
## GO:0016032 TFRC
## GO:0022414 RB1/CTNNA1/IGFBP2/ATM/MSH6/MSH2
## ID Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex 9 9/18
## GO:0044423 GO:0044423 virion component 0 0/18
## GO:0110165 GO:0110165 cellular anatomical entity 18 18/18
## geneID
## GO:0032991 RB1/CTNNA1/RBM15/ATM/TSC1/XBP1/MSH6/TFRC/MSH2
## GO:0044423
## GO:0110165 RB1/XIAP/CTNNA1/G6PD/IGFBP2/RBM15/ATM/FASN/INPP4B/TSC1/TTF1/VHL/PRDX1/XBP1/MSH6/TFRC/MSH2/PREX1
## ID Description Count GeneRatio
## GO:0003774 GO:0003774 cytoskeletal motor activity 1 1/60
## GO:0003824 GO:0003824 catalytic activity 39 39/60
## GO:0005198 GO:0005198 structural molecule activity 1 1/60
## GO:0005215 GO:0005215 transporter activity 2 2/60
## GO:0005488 GO:0005488 binding 60 60/60
## GO:0009055 GO:0009055 electron transfer activity 0 0/60
## geneID
## GO:0003774 MYH9
## GO:0003824 HSPA1A/AKT1/VHL/MTOR/MAPK8/CDKN1A/ATM/CASP8/PTEN/KRAS/NRAS/PTK2/PARP1/IGF1R/RAB25/CCND1/PIK3R1/XIAP/CHEK1/TUBA1B/KIT/NCOA3/EGFR/EZH2/PTGS2/MET/AKT2/PRKAA1/AXL/MSH2/CASP3/CCNE1/GAPDH/MSH6/PIK3CA/PRKCA/MAPK1/RAB11A/BRAF
## GO:0005198 TUBA1B
## GO:0005215 IGF1R/BCL2
## GO:0005488 HSPA1A/AKT1/VHL/MTOR/MAPK8/MYH9/CDKN1A/FOXO3/ATM/CASP8/MACC1/PTEN/KRAS/NRAS/PTK2/ETS1/PARP1/IGF1R/CCNE2/RAB25/CCND1/PIK3R1/XIAP/CHEK1/SRSF1/TUBA1B/STAT5A/KIT/NCOA3/EGFR/EZH2/PTGS2/MET/AKT2/YBX1/PRKAA1/PXN/BCL2/AXL/MYC/MSH2/CASP3/BCL2L11/CCNE1/YAP1/EIF4E/EIF4G1/GAPDH/MSH6/ITGA2/PIK3CA/PRKCA/MAPK1/TFRC/YWHAE/RAB11A/ANLN/RICTOR/TP53BP1/BRAF
## GO:0009055
## ID Description Count GeneRatio
## GO:0000003 GO:0000003 reproduction 22 22/60
## GO:0002376 GO:0002376 immune system process 33 33/60
## GO:0008152 GO:0008152 metabolic process 53 53/60
## GO:0009987 GO:0009987 cellular process 60 60/60
## GO:0016032 GO:0016032 viral process 7 7/60
## GO:0022414 GO:0022414 reproductive process 22 22/60
## geneID
## GO:0000003 AKT1/MTOR/MYH9/FOXO3/ATM/CASP8/PTEN/PARP1/IGF1R/CCNE2/KIT/EGFR/PTGS2/BCL2/AXL/MSH2/CASP3/BCL2L11/CCNE1/MSH6/ITGA2/PIK3CA
## GO:0002376 HSPA1A/AKT1/MTOR/MAPK8/MYH9/CDKN1A/FOXO3/ATM/CASP8/PTK2/ETS1/PARP1/IGF1R/PIK3R1/XIAP/KIT/EZH2/BCL2/AXL/MYC/MSH2/CASP3/BCL2L11/GAPDH/MSH6/ITGA2/PIK3CA/PRKCA/MAPK1/TFRC/YWHAE/TP53BP1/BRAF
## GO:0008152 HSPA1A/AKT1/VHL/MTOR/MAPK8/MYH9/CDKN1A/FOXO3/ATM/CASP8/MACC1/PTEN/KRAS/PTK2/ETS1/PARP1/IGF1R/CCNE2/CCND1/PIK3R1/XIAP/CHEK1/SRSF1/STAT5A/KIT/NCOA3/EGFR/EZH2/PTGS2/MET/AKT2/YBX1/PRKAA1/BCL2/AXL/MYC/MSH2/CASP3/CCNE1/YAP1/EIF4E/EIF4G1/GAPDH/MSH6/ITGA2/PIK3CA/PRKCA/MAPK1/TFRC/YWHAE/RICTOR/TP53BP1/BRAF
## GO:0009987 HSPA1A/AKT1/VHL/MTOR/MAPK8/MYH9/CDKN1A/FOXO3/ATM/CASP8/MACC1/PTEN/KRAS/NRAS/PTK2/ETS1/PARP1/IGF1R/CCNE2/RAB25/CCND1/PIK3R1/XIAP/CHEK1/SRSF1/TUBA1B/STAT5A/KIT/NCOA3/EGFR/EZH2/PTGS2/MET/AKT2/YBX1/PRKAA1/PXN/BCL2/AXL/MYC/MSH2/CASP3/BCL2L11/CCNE1/YAP1/EIF4E/EIF4G1/GAPDH/MSH6/ITGA2/PIK3CA/PRKCA/MAPK1/TFRC/YWHAE/RAB11A/ANLN/RICTOR/TP53BP1/BRAF
## GO:0016032 HSPA1A/AKT1/EGFR/BCL2/AXL/ITGA2/TFRC
## GO:0022414 AKT1/MTOR/MYH9/FOXO3/ATM/CASP8/PTEN/PARP1/IGF1R/CCNE2/KIT/EGFR/PTGS2/BCL2/AXL/MSH2/CASP3/BCL2L11/CCNE1/MSH6/ITGA2/PIK3CA
## ID Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex 45 45/60
## GO:0044423 GO:0044423 virion component 0 0/60
## GO:0110165 GO:0110165 cellular anatomical entity 60 60/60
## geneID
## GO:0032991 HSPA1A/AKT1/MTOR/MYH9/CDKN1A/FOXO3/ATM/CASP8/ETS1/PARP1/IGF1R/CCNE2/CCND1/PIK3R1/CHEK1/SRSF1/STAT5A/KIT/NCOA3/EGFR/EZH2/PTGS2/MET/YBX1/PRKAA1/PXN/BCL2/AXL/MYC/MSH2/CASP3/BCL2L11/CCNE1/YAP1/EIF4E/EIF4G1/GAPDH/MSH6/ITGA2/PIK3CA/PRKCA/TFRC/RAB11A/RICTOR/TP53BP1
## GO:0044423
## GO:0110165 HSPA1A/AKT1/VHL/MTOR/MAPK8/MYH9/CDKN1A/FOXO3/ATM/CASP8/MACC1/PTEN/KRAS/NRAS/PTK2/ETS1/PARP1/IGF1R/CCNE2/RAB25/CCND1/PIK3R1/XIAP/CHEK1/SRSF1/TUBA1B/STAT5A/KIT/NCOA3/EGFR/EZH2/PTGS2/MET/AKT2/YBX1/PRKAA1/PXN/BCL2/AXL/MYC/MSH2/CASP3/BCL2L11/CCNE1/YAP1/EIF4E/EIF4G1/GAPDH/MSH6/ITGA2/PIK3CA/PRKCA/MAPK1/TFRC/YWHAE/RAB11A/ANLN/RICTOR/TP53BP1/BRAF
## ID Description Count GeneRatio
## GO:0003774 GO:0003774 cytoskeletal motor activity 1 1/68
## GO:0003824 GO:0003824 catalytic activity 43 43/68
## GO:0005198 GO:0005198 structural molecule activity 1 1/68
## GO:0005215 GO:0005215 transporter activity 2 2/68
## GO:0005488 GO:0005488 binding 68 68/68
## GO:0009055 GO:0009055 electron transfer activity 0 0/68
## geneID
## GO:0003774 MYH9
## GO:0003824 XIAP/HSPA1A/AKT1/VHL/MTOR/MAPK8/CDKN1A/ATM/CASP8/PTEN/KRAS/NRAS/PTK2/PARP1/IGF1R/RAB25/CCND1/PIK3R1/CHEK1/TUBA1B/KIT/NCOA3/EGFR/EZH2/PTGS2/MET/AKT2/PRKAA1/AXL/MSH2/CASP3/CCNE1/GAPDH/MSH6/PIK3CA/PRKCA/MAPK1/RAB11A/BRAF/G6PD/FASN/INPP4B/PRDX1
## GO:0005198 TUBA1B
## GO:0005215 IGF1R/BCL2
## GO:0005488 RB1/XIAP/HSPA1A/AKT1/VHL/MTOR/MAPK8/ETS1/ARID1A/BID/MYH9/CDKN1A/FOXO3/ATM/CASP8/MACC1/PTEN/KRAS/NRAS/PTK2/PARP1/IGF1R/CCNE2/RAB25/CCND1/PIK3R1/CHEK1/SRSF1/TUBA1B/STAT5A/KIT/NCOA3/EGFR/EZH2/PTGS2/MET/AKT2/YBX1/PRKAA1/PXN/BCL2/AXL/MYC/MSH2/CASP3/BCL2L11/CCNE1/YAP1/EIF4E/EIF4G1/GAPDH/MSH6/ITGA2/PIK3CA/PRKCA/MAPK1/TFRC/YWHAE/RAB11A/GAB2/ANLN/RICTOR/TP53BP1/BRAF/G6PD/FASN/INPP4B/PRDX1
## GO:0009055
## ID Description Count GeneRatio
## GO:0000003 GO:0000003 reproduction 23 23/68
## GO:0002376 GO:0002376 immune system process 39 39/68
## GO:0008152 GO:0008152 metabolic process 60 60/68
## GO:0009987 GO:0009987 cellular process 68 68/68
## GO:0016032 GO:0016032 viral process 7 7/68
## GO:0022414 GO:0022414 reproductive process 23 23/68
## geneID
## GO:0000003 RB1/AKT1/MTOR/MYH9/FOXO3/ATM/CASP8/PTEN/PARP1/IGF1R/CCNE2/KIT/EGFR/PTGS2/BCL2/AXL/MSH2/CASP3/BCL2L11/CCNE1/MSH6/ITGA2/PIK3CA
## GO:0002376 RB1/XIAP/HSPA1A/AKT1/MTOR/MAPK8/ETS1/ARID1A/BID/MYH9/CDKN1A/FOXO3/ATM/CASP8/PTK2/PARP1/IGF1R/PIK3R1/KIT/EZH2/BCL2/AXL/MYC/MSH2/CASP3/BCL2L11/GAPDH/MSH6/ITGA2/PIK3CA/PRKCA/MAPK1/TFRC/YWHAE/GAB2/TP53BP1/BRAF/G6PD/PRDX1
## GO:0008152 RB1/XIAP/HSPA1A/AKT1/VHL/MTOR/MAPK8/ETS1/ARID1A/BID/MYH9/CDKN1A/FOXO3/ATM/CASP8/MACC1/PTEN/KRAS/PTK2/PARP1/IGF1R/CCNE2/CCND1/PIK3R1/CHEK1/SRSF1/STAT5A/KIT/NCOA3/EGFR/EZH2/PTGS2/MET/AKT2/YBX1/PRKAA1/BCL2/AXL/MYC/MSH2/CASP3/CCNE1/YAP1/EIF4E/EIF4G1/GAPDH/MSH6/ITGA2/PIK3CA/PRKCA/MAPK1/TFRC/YWHAE/RICTOR/TP53BP1/BRAF/G6PD/FASN/INPP4B/PRDX1
## GO:0009987 RB1/XIAP/HSPA1A/AKT1/VHL/MTOR/MAPK8/ETS1/ARID1A/BID/MYH9/CDKN1A/FOXO3/ATM/CASP8/MACC1/PTEN/KRAS/NRAS/PTK2/PARP1/IGF1R/CCNE2/RAB25/CCND1/PIK3R1/CHEK1/SRSF1/TUBA1B/STAT5A/KIT/NCOA3/EGFR/EZH2/PTGS2/MET/AKT2/YBX1/PRKAA1/PXN/BCL2/AXL/MYC/MSH2/CASP3/BCL2L11/CCNE1/YAP1/EIF4E/EIF4G1/GAPDH/MSH6/ITGA2/PIK3CA/PRKCA/MAPK1/TFRC/YWHAE/RAB11A/GAB2/ANLN/RICTOR/TP53BP1/BRAF/G6PD/FASN/INPP4B/PRDX1
## GO:0016032 HSPA1A/AKT1/EGFR/BCL2/AXL/ITGA2/TFRC
## GO:0022414 RB1/AKT1/MTOR/MYH9/FOXO3/ATM/CASP8/PTEN/PARP1/IGF1R/CCNE2/KIT/EGFR/PTGS2/BCL2/AXL/MSH2/CASP3/BCL2L11/CCNE1/MSH6/ITGA2/PIK3CA
## ID Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex 47 47/68
## GO:0044423 GO:0044423 virion component 0 0/68
## GO:0110165 GO:0110165 cellular anatomical entity 68 68/68
## geneID
## GO:0032991 RB1/HSPA1A/AKT1/MTOR/ETS1/ARID1A/MYH9/CDKN1A/FOXO3/ATM/CASP8/PARP1/IGF1R/CCNE2/CCND1/PIK3R1/CHEK1/SRSF1/STAT5A/KIT/NCOA3/EGFR/EZH2/PTGS2/MET/YBX1/PRKAA1/PXN/BCL2/AXL/MYC/MSH2/CASP3/BCL2L11/CCNE1/YAP1/EIF4E/EIF4G1/GAPDH/MSH6/ITGA2/PIK3CA/PRKCA/TFRC/RAB11A/RICTOR/TP53BP1
## GO:0044423
## GO:0110165 RB1/XIAP/HSPA1A/AKT1/VHL/MTOR/MAPK8/ETS1/ARID1A/BID/MYH9/CDKN1A/FOXO3/ATM/CASP8/MACC1/PTEN/KRAS/NRAS/PTK2/PARP1/IGF1R/CCNE2/RAB25/CCND1/PIK3R1/CHEK1/SRSF1/TUBA1B/STAT5A/KIT/NCOA3/EGFR/EZH2/PTGS2/MET/AKT2/YBX1/PRKAA1/PXN/BCL2/AXL/MYC/MSH2/CASP3/BCL2L11/CCNE1/YAP1/EIF4E/EIF4G1/GAPDH/MSH6/ITGA2/PIK3CA/PRKCA/MAPK1/TFRC/YWHAE/RAB11A/GAB2/ANLN/RICTOR/TP53BP1/BRAF/G6PD/FASN/INPP4B/PRDX1
## ID Description Count GeneRatio
## GO:0003774 GO:0003774 cytoskeletal motor activity 0 0/28
## GO:0003824 GO:0003824 catalytic activity 13 13/28
## GO:0005198 GO:0005198 structural molecule activity 0 0/28
## GO:0005215 GO:0005215 transporter activity 1 1/28
## GO:0005488 GO:0005488 binding 28 28/28
## GO:0009055 GO:0009055 electron transfer activity 0 0/28
## geneID
## GO:0003774
## GO:0003824 AKT2/AKT1/XIAP/MAPK8/PTEN/KRAS/NRAS/PTK2/ATM/CCND1/CDKN1A/NCOA3/VHL
## GO:0005198
## GO:0005215 BCL2
## GO:0005488 AKT2/BCL2/MYC/AKT1/BCL2L1/RB1/XIAP/ETS1/MAPK8/ARID1A/BID/PTEN/KRAS/NRAS/PTK2/ATM/YWHAZ/CCND1/CDKN1A/NF2/NCOA3/ITGA2/GAB2/RBM15/TSC1/TTF1/VHL/PREX1
## GO:0009055
## ID Description Count GeneRatio
## GO:0000003 GO:0000003 reproduction 7 7/28
## GO:0002376 GO:0002376 immune system process 18 18/28
## GO:0008152 GO:0008152 metabolic process 25 25/28
## GO:0009987 GO:0009987 cellular process 28 28/28
## GO:0016032 GO:0016032 viral process 3 3/28
## GO:0022414 GO:0022414 reproductive process 7 7/28
## geneID
## GO:0000003 BCL2/AKT1/BCL2L1/RB1/PTEN/ATM/ITGA2
## GO:0002376 BCL2/MYC/AKT1/RB1/XIAP/ETS1/MAPK8/ARID1A/BID/PTK2/ATM/YWHAZ/CDKN1A/ITGA2/GAB2/RBM15/TSC1/PREX1
## GO:0008152 AKT2/BCL2/MYC/AKT1/RB1/XIAP/ETS1/MAPK8/ARID1A/BID/PTEN/KRAS/PTK2/ATM/YWHAZ/CCND1/CDKN1A/NF2/NCOA3/ITGA2/RBM15/TSC1/TTF1/VHL/PREX1
## GO:0009987 AKT2/BCL2/MYC/AKT1/BCL2L1/RB1/XIAP/ETS1/MAPK8/ARID1A/BID/PTEN/KRAS/NRAS/PTK2/ATM/YWHAZ/CCND1/CDKN1A/NF2/NCOA3/ITGA2/GAB2/RBM15/TSC1/TTF1/VHL/PREX1
## GO:0016032 BCL2/AKT1/ITGA2
## GO:0022414 BCL2/AKT1/BCL2L1/RB1/PTEN/ATM/ITGA2
## ID Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex 14 14/28
## GO:0044423 GO:0044423 virion component 0 0/28
## GO:0110165 GO:0110165 cellular anatomical entity 28 28/28
## geneID
## GO:0032991 BCL2/MYC/AKT1/BCL2L1/RB1/ETS1/ARID1A/ATM/CCND1/CDKN1A/NCOA3/ITGA2/RBM15/TSC1
## GO:0044423
## GO:0110165 AKT2/BCL2/MYC/AKT1/BCL2L1/RB1/XIAP/ETS1/MAPK8/ARID1A/BID/PTEN/KRAS/NRAS/PTK2/ATM/YWHAZ/CCND1/CDKN1A/NF2/NCOA3/ITGA2/GAB2/RBM15/TSC1/TTF1/VHL/PREX1
## ID Description Count GeneRatio geneID
## GO:0003774 GO:0003774 cytoskeletal motor activity 0 0/0
## GO:0003824 GO:0003824 catalytic activity 0 0/0
## GO:0005198 GO:0005198 structural molecule activity 0 0/0
## GO:0005215 GO:0005215 transporter activity 0 0/0
## GO:0005488 GO:0005488 binding 0 0/0
## GO:0009055 GO:0009055 electron transfer activity 0 0/0
## ID Description Count GeneRatio geneID
## GO:0000003 GO:0000003 reproduction 0 0/0
## GO:0002376 GO:0002376 immune system process 0 0/0
## GO:0008152 GO:0008152 metabolic process 0 0/0
## GO:0009987 GO:0009987 cellular process 0 0/0
## GO:0016032 GO:0016032 viral process 0 0/0
## GO:0022414 GO:0022414 reproductive process 0 0/0
## ID Description Count GeneRatio geneID
## GO:0032991 GO:0032991 protein-containing complex 0 0/0
## GO:0044423 GO:0044423 virion component 0 0/0
## GO:0110165 GO:0110165 cellular anatomical entity 0 0/0
## ID Description Count GeneRatio
## GO:0003774 GO:0003774 cytoskeletal motor activity 1 1/22
## GO:0003824 GO:0003824 catalytic activity 11 11/22
## GO:0005198 GO:0005198 structural molecule activity 1 1/22
## GO:0005215 GO:0005215 transporter activity 0 0/22
## GO:0005488 GO:0005488 binding 22 22/22
## GO:0009055 GO:0009055 electron transfer activity 0 0/22
## geneID
## GO:0003774 MYH11
## GO:0003824 CDK1/G6PD/ATM/BRCA2/FASN/INPP4B/VHL/PRDX1/GAPDH/MSH6/MSH2
## GO:0005198 MYH11
## GO:0005215
## GO:0005488 STMN1/CDK1/CCNB1/G6PD/IGFBP2/RBM15/GATA3/ATM/BRCA2/FASN/INPP4B/TSC1/TTF1/VHL/PRDX1/XBP1/GAPDH/MSH6/MYH11/TFRC/MSH2/PREX1
## GO:0009055
## ID Description Count GeneRatio
## GO:0000003 GO:0000003 reproduction 7 7/22
## GO:0002376 GO:0002376 immune system process 13 13/22
## GO:0008152 GO:0008152 metabolic process 19 19/22
## GO:0009987 GO:0009987 cellular process 22 22/22
## GO:0016032 GO:0016032 viral process 2 2/22
## GO:0022414 GO:0022414 reproductive process 7 7/22
## geneID
## GO:0000003 CDK1/IGFBP2/GATA3/ATM/BRCA2/MSH6/MSH2
## GO:0002376 G6PD/IGFBP2/RBM15/GATA3/ATM/TSC1/PRDX1/XBP1/GAPDH/MSH6/TFRC/MSH2/PREX1
## GO:0008152 CDK1/CCNB1/G6PD/RBM15/GATA3/ATM/BRCA2/FASN/INPP4B/TSC1/TTF1/VHL/PRDX1/XBP1/GAPDH/MSH6/TFRC/MSH2/PREX1
## GO:0009987 STMN1/CDK1/CCNB1/G6PD/IGFBP2/RBM15/GATA3/ATM/BRCA2/FASN/INPP4B/TSC1/TTF1/VHL/PRDX1/XBP1/GAPDH/MSH6/MYH11/TFRC/MSH2/PREX1
## GO:0016032 CDK1/TFRC
## GO:0022414 CDK1/IGFBP2/GATA3/ATM/BRCA2/MSH6/MSH2
## ID Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex 13 13/22
## GO:0044423 GO:0044423 virion component 0 0/22
## GO:0110165 GO:0110165 cellular anatomical entity 22 22/22
## geneID
## GO:0032991 CDK1/CCNB1/RBM15/GATA3/ATM/BRCA2/TSC1/XBP1/GAPDH/MSH6/MYH11/TFRC/MSH2
## GO:0044423
## GO:0110165 STMN1/CDK1/CCNB1/G6PD/IGFBP2/RBM15/GATA3/ATM/BRCA2/FASN/INPP4B/TSC1/TTF1/VHL/PRDX1/XBP1/GAPDH/MSH6/MYH11/TFRC/MSH2/PREX1
## ID Description Count GeneRatio
## GO:0003774 GO:0003774 cytoskeletal motor activity 1 1/73
## GO:0003824 GO:0003824 catalytic activity 43 43/73
## GO:0005198 GO:0005198 structural molecule activity 1 1/73
## GO:0005215 GO:0005215 transporter activity 2 2/73
## GO:0005488 GO:0005488 binding 73 73/73
## GO:0009055 GO:0009055 electron transfer activity 0 0/73
## geneID
## GO:0003774 MYH9
## GO:0003824 XIAP/HSPA1A/AKT1/VHL/MTOR/MAPK8/CDKN1A/ATM/CASP8/PTEN/KRAS/NRAS/PTK2/PARP1/IGF1R/RAB25/CCND1/PIK3R1/CHEK1/TUBA1B/KIT/NCOA3/EGFR/EZH2/PTGS2/MET/AKT2/PRKAA1/CASP9/AXL/MSH2/CASP3/CCNE1/MAPK9/RAF1/GAPDH/MSH6/PIK3CA/PRKCA/MAPK1/MAPK3/RAB11A/BRAF
## GO:0005198 TUBA1B
## GO:0005215 IGF1R/BCL2
## GO:0005488 RB1/XIAP/HSPA1A/AKT1/VHL/MTOR/MAPK8/ETS1/ARID1A/BID/MYH9/CDKN1A/FOXO3/ATM/CASP8/MACC1/PTEN/KRAS/NRAS/PTK2/PARP1/IGF1R/CCNE2/RAB25/CCND1/PIK3R1/CHEK1/SRSF1/TUBA1B/STAT5A/KIT/NCOA3/EGFR/EZH2/PTGS2/MET/AKT2/YBX1/PRKAA1/PXN/BCL2/E2F1/CASP9/AXL/CDKN2A/MYC/MSH2/CASP3/BCL2L11/CCNE1/MAPK9/RAF1/YAP1/BCL2L1/DVL3/EIF4E/EIF4G1/GAPDH/MSH6/ITGA2/SMAD3/PIK3CA/PRKCA/MAPK1/MAPK3/TFRC/YWHAE/RAB11A/GAB2/ANLN/RICTOR/TP53BP1/BRAF
## GO:0009055
## ID Description Count GeneRatio
## GO:0000003 GO:0000003 reproduction 24 24/73
## GO:0002376 GO:0002376 immune system process 41 41/73
## GO:0008152 GO:0008152 metabolic process 64 64/73
## GO:0009987 GO:0009987 cellular process 73 73/73
## GO:0016032 GO:0016032 viral process 7 7/73
## GO:0022414 GO:0022414 reproductive process 24 24/73
## geneID
## GO:0000003 RB1/AKT1/MTOR/MYH9/FOXO3/ATM/CASP8/PTEN/PARP1/IGF1R/CCNE2/KIT/EGFR/PTGS2/BCL2/AXL/MSH2/CASP3/BCL2L11/CCNE1/BCL2L1/MSH6/ITGA2/PIK3CA
## GO:0002376 RB1/XIAP/HSPA1A/AKT1/MTOR/MAPK8/ETS1/ARID1A/BID/MYH9/CDKN1A/FOXO3/ATM/CASP8/PTK2/PARP1/IGF1R/PIK3R1/KIT/EZH2/BCL2/AXL/MYC/MSH2/CASP3/BCL2L11/MAPK9/RAF1/GAPDH/MSH6/ITGA2/SMAD3/PIK3CA/PRKCA/MAPK1/MAPK3/TFRC/YWHAE/GAB2/TP53BP1/BRAF
## GO:0008152 RB1/XIAP/HSPA1A/AKT1/VHL/MTOR/MAPK8/ETS1/ARID1A/BID/MYH9/CDKN1A/FOXO3/ATM/CASP8/MACC1/PTEN/KRAS/PTK2/PARP1/IGF1R/CCNE2/CCND1/PIK3R1/CHEK1/SRSF1/STAT5A/KIT/NCOA3/EGFR/EZH2/PTGS2/MET/AKT2/YBX1/PRKAA1/BCL2/E2F1/CASP9/AXL/CDKN2A/MYC/MSH2/CASP3/CCNE1/MAPK9/RAF1/YAP1/DVL3/EIF4E/EIF4G1/GAPDH/MSH6/ITGA2/SMAD3/PIK3CA/PRKCA/MAPK1/MAPK3/TFRC/YWHAE/RICTOR/TP53BP1/BRAF
## GO:0009987 RB1/XIAP/HSPA1A/AKT1/VHL/MTOR/MAPK8/ETS1/ARID1A/BID/MYH9/CDKN1A/FOXO3/ATM/CASP8/MACC1/PTEN/KRAS/NRAS/PTK2/PARP1/IGF1R/CCNE2/RAB25/CCND1/PIK3R1/CHEK1/SRSF1/TUBA1B/STAT5A/KIT/NCOA3/EGFR/EZH2/PTGS2/MET/AKT2/YBX1/PRKAA1/PXN/BCL2/E2F1/CASP9/AXL/CDKN2A/MYC/MSH2/CASP3/BCL2L11/CCNE1/MAPK9/RAF1/YAP1/BCL2L1/DVL3/EIF4E/EIF4G1/GAPDH/MSH6/ITGA2/SMAD3/PIK3CA/PRKCA/MAPK1/MAPK3/TFRC/YWHAE/RAB11A/GAB2/ANLN/RICTOR/TP53BP1/BRAF
## GO:0016032 HSPA1A/AKT1/EGFR/BCL2/AXL/ITGA2/TFRC
## GO:0022414 RB1/AKT1/MTOR/MYH9/FOXO3/ATM/CASP8/PTEN/PARP1/IGF1R/CCNE2/KIT/EGFR/PTGS2/BCL2/AXL/MSH2/CASP3/BCL2L11/CCNE1/BCL2L1/MSH6/ITGA2/PIK3CA
## ID Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex 53 53/73
## GO:0044423 GO:0044423 virion component 0 0/73
## GO:0110165 GO:0110165 cellular anatomical entity 73 73/73
## geneID
## GO:0032991 RB1/HSPA1A/AKT1/MTOR/ETS1/ARID1A/MYH9/CDKN1A/FOXO3/ATM/CASP8/PARP1/IGF1R/CCNE2/CCND1/PIK3R1/CHEK1/SRSF1/STAT5A/KIT/NCOA3/EGFR/EZH2/PTGS2/MET/YBX1/PRKAA1/PXN/BCL2/E2F1/CASP9/AXL/CDKN2A/MYC/MSH2/CASP3/BCL2L11/CCNE1/YAP1/BCL2L1/DVL3/EIF4E/EIF4G1/GAPDH/MSH6/ITGA2/SMAD3/PIK3CA/PRKCA/TFRC/RAB11A/RICTOR/TP53BP1
## GO:0044423
## GO:0110165 RB1/XIAP/HSPA1A/AKT1/VHL/MTOR/MAPK8/ETS1/ARID1A/BID/MYH9/CDKN1A/FOXO3/ATM/CASP8/MACC1/PTEN/KRAS/NRAS/PTK2/PARP1/IGF1R/CCNE2/RAB25/CCND1/PIK3R1/CHEK1/SRSF1/TUBA1B/STAT5A/KIT/NCOA3/EGFR/EZH2/PTGS2/MET/AKT2/YBX1/PRKAA1/PXN/BCL2/E2F1/CASP9/AXL/CDKN2A/MYC/MSH2/CASP3/BCL2L11/CCNE1/MAPK9/RAF1/YAP1/BCL2L1/DVL3/EIF4E/EIF4G1/GAPDH/MSH6/ITGA2/SMAD3/PIK3CA/PRKCA/MAPK1/MAPK3/TFRC/YWHAE/RAB11A/GAB2/ANLN/RICTOR/TP53BP1/BRAF
## ID Description Count GeneRatio
## GO:0003774 GO:0003774 cytoskeletal motor activity 0 0/36
## GO:0003824 GO:0003824 catalytic activity 18 18/36
## GO:0005198 GO:0005198 structural molecule activity 1 1/36
## GO:0005215 GO:0005215 transporter activity 2 2/36
## GO:0005488 GO:0005488 binding 36 36/36
## GO:0009055 GO:0009055 electron transfer activity 0 0/36
## geneID
## GO:0003774
## GO:0003824 MET/AKT2/G6PD/KRAS/CCND1/AKT1/IGF1R/XIAP/MAPK8/PTEN/NRAS/PTK2/ATM/MAPK1/CDKN1A/NCOA3/CHEK1/XRCC1
## GO:0005198 FN1
## GO:0005215 BCL2/IGF1R
## GO:0005488 ESR1/MET/AKT2/G6PD/BCL2/KRAS/CCND1/NOTCH3/AKT1/IGF1R/MYC/BCL2L1/RB1/XIAP/ETS1/MAPK8/ARID1A/BID/PTEN/NRAS/PTK2/ATM/YWHAZ/ITGA2/MAPK1/PXN/YWHAB/CDKN1A/STAT5A/NF2/NCOA3/FOXO3/CHEK1/FN1/XRCC1/GAB2
## GO:0009055
## ID Description Count GeneRatio
## GO:0000003 GO:0000003 reproduction 10 10/36
## GO:0002376 GO:0002376 immune system process 21 21/36
## GO:0008152 GO:0008152 metabolic process 32 32/36
## GO:0009987 GO:0009987 cellular process 36 36/36
## GO:0016032 GO:0016032 viral process 3 3/36
## GO:0022414 GO:0022414 reproductive process 10 10/36
## geneID
## GO:0000003 ESR1/BCL2/AKT1/IGF1R/BCL2L1/RB1/PTEN/ATM/ITGA2/FOXO3
## GO:0002376 ESR1/G6PD/BCL2/AKT1/IGF1R/MYC/RB1/XIAP/ETS1/MAPK8/ARID1A/BID/PTK2/ATM/YWHAZ/ITGA2/MAPK1/CDKN1A/FOXO3/FN1/GAB2
## GO:0008152 ESR1/MET/AKT2/G6PD/BCL2/KRAS/CCND1/NOTCH3/AKT1/IGF1R/MYC/RB1/XIAP/ETS1/MAPK8/ARID1A/BID/PTEN/PTK2/ATM/YWHAZ/ITGA2/MAPK1/YWHAB/CDKN1A/STAT5A/NF2/NCOA3/FOXO3/CHEK1/FN1/XRCC1
## GO:0009987 ESR1/MET/AKT2/G6PD/BCL2/KRAS/CCND1/NOTCH3/AKT1/IGF1R/MYC/BCL2L1/RB1/XIAP/ETS1/MAPK8/ARID1A/BID/PTEN/NRAS/PTK2/ATM/YWHAZ/ITGA2/MAPK1/PXN/YWHAB/CDKN1A/STAT5A/NF2/NCOA3/FOXO3/CHEK1/FN1/XRCC1/GAB2
## GO:0016032 BCL2/AKT1/ITGA2
## GO:0022414 ESR1/BCL2/AKT1/IGF1R/BCL2L1/RB1/PTEN/ATM/ITGA2/FOXO3
## ID Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex 22 22/36
## GO:0044423 GO:0044423 virion component 0 0/36
## GO:0110165 GO:0110165 cellular anatomical entity 36 36/36
## geneID
## GO:0032991 ESR1/MET/BCL2/CCND1/NOTCH3/AKT1/IGF1R/MYC/BCL2L1/RB1/ETS1/ARID1A/ATM/ITGA2/PXN/CDKN1A/STAT5A/NCOA3/FOXO3/CHEK1/FN1/XRCC1
## GO:0044423
## GO:0110165 ESR1/MET/AKT2/G6PD/BCL2/KRAS/CCND1/NOTCH3/AKT1/IGF1R/MYC/BCL2L1/RB1/XIAP/ETS1/MAPK8/ARID1A/BID/PTEN/NRAS/PTK2/ATM/YWHAZ/ITGA2/MAPK1/PXN/YWHAB/CDKN1A/STAT5A/NF2/NCOA3/FOXO3/CHEK1/FN1/XRCC1/GAB2
## ID Description Count GeneRatio geneID
## GO:0003774 GO:0003774 cytoskeletal motor activity 0 0/1
## GO:0003824 GO:0003824 catalytic activity 0 0/1
## GO:0005198 GO:0005198 structural molecule activity 0 0/1
## GO:0005215 GO:0005215 transporter activity 0 0/1
## GO:0005488 GO:0005488 binding 1 1/1 PEA15
## GO:0009055 GO:0009055 electron transfer activity 0 0/1
## ID Description Count GeneRatio geneID
## GO:0000003 GO:0000003 reproduction 0 0/1
## GO:0002376 GO:0002376 immune system process 0 0/1
## GO:0008152 GO:0008152 metabolic process 0 0/1
## GO:0009987 GO:0009987 cellular process 1 1/1 PEA15
## GO:0016032 GO:0016032 viral process 0 0/1
## GO:0022414 GO:0022414 reproductive process 0 0/1
## ID Description Count GeneRatio geneID
## GO:0032991 GO:0032991 protein-containing complex 1 1/1 PEA15
## GO:0044423 GO:0044423 virion component 0 0/1
## GO:0110165 GO:0110165 cellular anatomical entity 1 1/1 PEA15
## ID Description Count GeneRatio geneID
## GO:0003774 GO:0003774 cytoskeletal motor activity 0 0/1
## GO:0003824 GO:0003824 catalytic activity 1 1/1 PARP1
## GO:0005198 GO:0005198 structural molecule activity 0 0/1
## GO:0005215 GO:0005215 transporter activity 0 0/1
## GO:0005488 GO:0005488 binding 1 1/1 PARP1
## GO:0009055 GO:0009055 electron transfer activity 0 0/1
## ID Description Count GeneRatio geneID
## GO:0000003 GO:0000003 reproduction 1 1/1 PARP1
## GO:0002376 GO:0002376 immune system process 1 1/1 PARP1
## GO:0008152 GO:0008152 metabolic process 1 1/1 PARP1
## GO:0009987 GO:0009987 cellular process 1 1/1 PARP1
## GO:0016032 GO:0016032 viral process 0 0/1
## GO:0022414 GO:0022414 reproductive process 1 1/1 PARP1
## ID Description Count GeneRatio geneID
## GO:0032991 GO:0032991 protein-containing complex 1 1/1 PARP1
## GO:0044423 GO:0044423 virion component 0 0/1
## GO:0110165 GO:0110165 cellular anatomical entity 1 1/1 PARP1
## ID Description Count GeneRatio
## GO:0003774 GO:0003774 cytoskeletal motor activity 1 1/57
## GO:0003824 GO:0003824 catalytic activity 26 26/57
## GO:0005198 GO:0005198 structural molecule activity 3 3/57
## GO:0005215 GO:0005215 transporter activity 2 2/57
## GO:0005488 GO:0005488 binding 57 57/57
## GO:0009055 GO:0009055 electron transfer activity 0 0/57
## geneID
## GO:0003774 MYH11
## GO:0003824 XIAP/AKT1/ACACA/PTEN/PARP1/EEF2/IGF1R/MAPK1/GSK3A/FASN/PRKCA/RAB11A/CDK1/TYMS/MSH6/PDK1/G6PD/ASNS/ATM/BRCA2/INPP4B/ACVRL1/VHL/PRDX1/GAPDH/MSH2
## GO:0005198 CTNNA1/COL6A1/MYH11
## GO:0005215 BCL2/IGF1R
## GO:0005488 RB1/XIAP/AKT1/ACACA/PTEN/BCL2/BCL2L11/PARP1/CTNNA1/EEF2/GATA3/NRG1/IGF1R/MAPK1/TFRC/NDRG1/AKT1S1/RICTOR/TP53BP1/GSK3A/CDH2/FASN/PRKCA/ANLN/STMN1/RAB11A/ETS1/CDK1/TYMS/MSH6/CCNB1/PDK1/FOXM1/COL6A1/STAT5A/YWHAB/ANXA1/PREX1/SQSTM1/G6PD/IGFBP2/ASNS/RBM15/PEA15/ATM/BRCA2/INPP4B/ACVRL1/TSC1/TTF1/VHL/AR/PRDX1/XBP1/GAPDH/MYH11/MSH2
## GO:0009055
## ID Description Count GeneRatio
## GO:0000003 GO:0000003 reproduction 18 18/57
## GO:0002376 GO:0002376 immune system process 27 27/57
## GO:0008152 GO:0008152 metabolic process 47 47/57
## GO:0009987 GO:0009987 cellular process 57 57/57
## GO:0016032 GO:0016032 viral process 5 5/57
## GO:0022414 GO:0022414 reproductive process 18 18/57
## geneID
## GO:0000003 RB1/AKT1/PTEN/BCL2/BCL2L11/PARP1/CTNNA1/GATA3/IGF1R/GSK3A/CDK1/MSH6/COL6A1/IGFBP2/ATM/BRCA2/AR/MSH2
## GO:0002376 RB1/XIAP/AKT1/BCL2/BCL2L11/PARP1/GATA3/IGF1R/MAPK1/TFRC/NDRG1/TP53BP1/PRKCA/ETS1/MSH6/ANXA1/PREX1/SQSTM1/G6PD/IGFBP2/RBM15/ATM/TSC1/PRDX1/XBP1/GAPDH/MSH2
## GO:0008152 RB1/XIAP/AKT1/ACACA/PTEN/BCL2/PARP1/EEF2/GATA3/NRG1/IGF1R/MAPK1/TFRC/AKT1S1/RICTOR/TP53BP1/GSK3A/FASN/PRKCA/ETS1/CDK1/TYMS/MSH6/CCNB1/PDK1/FOXM1/COL6A1/STAT5A/YWHAB/ANXA1/PREX1/SQSTM1/G6PD/ASNS/RBM15/ATM/BRCA2/INPP4B/ACVRL1/TSC1/TTF1/VHL/AR/PRDX1/XBP1/GAPDH/MSH2
## GO:0009987 RB1/XIAP/AKT1/ACACA/PTEN/BCL2/BCL2L11/PARP1/CTNNA1/EEF2/GATA3/NRG1/IGF1R/MAPK1/TFRC/NDRG1/AKT1S1/RICTOR/TP53BP1/GSK3A/CDH2/FASN/PRKCA/ANLN/STMN1/RAB11A/ETS1/CDK1/TYMS/MSH6/CCNB1/PDK1/FOXM1/COL6A1/STAT5A/YWHAB/ANXA1/PREX1/SQSTM1/G6PD/IGFBP2/ASNS/RBM15/PEA15/ATM/BRCA2/INPP4B/ACVRL1/TSC1/TTF1/VHL/AR/PRDX1/XBP1/GAPDH/MYH11/MSH2
## GO:0016032 AKT1/BCL2/TFRC/GSK3A/CDK1
## GO:0022414 RB1/AKT1/PTEN/BCL2/BCL2L11/PARP1/CTNNA1/GATA3/IGF1R/GSK3A/CDK1/MSH6/COL6A1/IGFBP2/ATM/BRCA2/AR/MSH2
## ID Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex 36 36/57
## GO:0044423 GO:0044423 virion component 0 0/57
## GO:0110165 GO:0110165 cellular anatomical entity 57 57/57
## geneID
## GO:0032991 RB1/AKT1/BCL2/BCL2L11/PARP1/CTNNA1/EEF2/GATA3/IGF1R/TFRC/AKT1S1/RICTOR/TP53BP1/GSK3A/CDH2/PRKCA/RAB11A/ETS1/CDK1/MSH6/CCNB1/PDK1/FOXM1/COL6A1/STAT5A/RBM15/PEA15/ATM/BRCA2/ACVRL1/TSC1/AR/XBP1/GAPDH/MYH11/MSH2
## GO:0044423
## GO:0110165 RB1/XIAP/AKT1/ACACA/PTEN/BCL2/BCL2L11/PARP1/CTNNA1/EEF2/GATA3/NRG1/IGF1R/MAPK1/TFRC/NDRG1/AKT1S1/RICTOR/TP53BP1/GSK3A/CDH2/FASN/PRKCA/ANLN/STMN1/RAB11A/ETS1/CDK1/TYMS/MSH6/CCNB1/PDK1/FOXM1/COL6A1/STAT5A/YWHAB/ANXA1/PREX1/SQSTM1/G6PD/IGFBP2/ASNS/RBM15/PEA15/ATM/BRCA2/INPP4B/ACVRL1/TSC1/TTF1/VHL/AR/PRDX1/XBP1/GAPDH/MYH11/MSH2
## ID Description Count GeneRatio
## GO:0003774 GO:0003774 cytoskeletal motor activity 1 1/83
## GO:0003824 GO:0003824 catalytic activity 46 46/83
## GO:0005198 GO:0005198 structural molecule activity 2 2/83
## GO:0005215 GO:0005215 transporter activity 2 2/83
## GO:0005488 GO:0005488 binding 83 83/83
## GO:0009055 GO:0009055 electron transfer activity 0 0/83
## geneID
## GO:0003774 MYH9
## GO:0003824 MET/G6PD/KRAS/CCND1/AKT1/IGF1R/XIAP/CDKN1A/HSPA1A/VHL/MTOR/MAPK8/ATM/CASP8/PTEN/NRAS/PTK2/PARP1/RAB25/RAD51/ERCC1/PIK3R1/CHEK1/TUBA1B/KIT/NCOA3/EGFR/EZH2/PTGS2/AKT2/PRKAA1/CASP9/AXL/MSH2/CASP3/CCNE1/MAPK9/RAF1/GAPDH/MSH6/PIK3CA/PRKCA/MAPK1/MAPK3/RAB11A/BRAF
## GO:0005198 TUBA1B/FN1
## GO:0005215 BCL2/IGF1R
## GO:0005488 ESR1/MET/G6PD/BCL2/KRAS/CCND1/NOTCH3/AKT1/IGF1R/RB1/XIAP/CDKN1A/HSPA1A/VHL/MTOR/MAPK8/ETS1/ARID1A/BID/MYH9/FOXO3/ATM/CASP8/MACC1/PTEN/NRAS/PTK2/PARP1/CCNE2/RAB25/AR/EIF4E/MAPT/RAD51/ERCC1/PIK3R1/CHEK1/SRSF1/TUBA1B/STAT5A/CDKN1B/BCL2L11/KIT/NCOA3/EGFR/EZH2/PTGS2/AKT2/YBX1/PRKAA1/PXN/E2F1/CASP9/AXL/CDKN2A/MYC/MSH2/CASP3/CCNE1/MAPK9/RAF1/YAP1/BCL2L1/DVL3/EIF4G1/FN1/GAPDH/MSH6/ITGA2/SMAD3/SMAD4/PIK3CA/PRKCA/MAPK1/MAPK3/TFRC/YWHAE/RAB11A/GAB2/ANLN/RICTOR/TP53BP1/BRAF
## GO:0009055
## ID Description Count GeneRatio
## GO:0000003 GO:0000003 reproduction 30 30/83
## GO:0002376 GO:0002376 immune system process 46 46/83
## GO:0008152 GO:0008152 metabolic process 74 74/83
## GO:0009987 GO:0009987 cellular process 83 83/83
## GO:0016032 GO:0016032 viral process 7 7/83
## GO:0022414 GO:0022414 reproductive process 30 30/83
## geneID
## GO:0000003 ESR1/BCL2/AKT1/IGF1R/RB1/MTOR/MYH9/FOXO3/ATM/CASP8/PTEN/PARP1/CCNE2/AR/RAD51/ERCC1/CDKN1B/BCL2L11/KIT/EGFR/PTGS2/AXL/MSH2/CASP3/CCNE1/BCL2L1/MSH6/ITGA2/SMAD4/PIK3CA
## GO:0002376 ESR1/G6PD/BCL2/AKT1/IGF1R/RB1/XIAP/CDKN1A/HSPA1A/MTOR/MAPK8/ETS1/ARID1A/BID/MYH9/FOXO3/ATM/CASP8/PTK2/PARP1/MAPT/ERCC1/PIK3R1/BCL2L11/KIT/EZH2/AXL/MYC/MSH2/CASP3/MAPK9/RAF1/FN1/GAPDH/MSH6/ITGA2/SMAD3/PIK3CA/PRKCA/MAPK1/MAPK3/TFRC/YWHAE/GAB2/TP53BP1/BRAF
## GO:0008152 ESR1/MET/G6PD/BCL2/KRAS/CCND1/NOTCH3/AKT1/IGF1R/RB1/XIAP/CDKN1A/HSPA1A/VHL/MTOR/MAPK8/ETS1/ARID1A/BID/MYH9/FOXO3/ATM/CASP8/MACC1/PTEN/PTK2/PARP1/CCNE2/AR/EIF4E/MAPT/RAD51/ERCC1/PIK3R1/CHEK1/SRSF1/STAT5A/CDKN1B/KIT/NCOA3/EGFR/EZH2/PTGS2/AKT2/YBX1/PRKAA1/E2F1/CASP9/AXL/CDKN2A/MYC/MSH2/CASP3/CCNE1/MAPK9/RAF1/YAP1/DVL3/EIF4G1/FN1/GAPDH/MSH6/ITGA2/SMAD3/SMAD4/PIK3CA/PRKCA/MAPK1/MAPK3/TFRC/YWHAE/RICTOR/TP53BP1/BRAF
## GO:0009987 ESR1/MET/G6PD/BCL2/KRAS/CCND1/NOTCH3/AKT1/IGF1R/RB1/XIAP/CDKN1A/HSPA1A/VHL/MTOR/MAPK8/ETS1/ARID1A/BID/MYH9/FOXO3/ATM/CASP8/MACC1/PTEN/NRAS/PTK2/PARP1/CCNE2/RAB25/AR/EIF4E/MAPT/RAD51/ERCC1/PIK3R1/CHEK1/SRSF1/TUBA1B/STAT5A/CDKN1B/BCL2L11/KIT/NCOA3/EGFR/EZH2/PTGS2/AKT2/YBX1/PRKAA1/PXN/E2F1/CASP9/AXL/CDKN2A/MYC/MSH2/CASP3/CCNE1/MAPK9/RAF1/YAP1/BCL2L1/DVL3/EIF4G1/FN1/GAPDH/MSH6/ITGA2/SMAD3/SMAD4/PIK3CA/PRKCA/MAPK1/MAPK3/TFRC/YWHAE/RAB11A/GAB2/ANLN/RICTOR/TP53BP1/BRAF
## GO:0016032 BCL2/AKT1/HSPA1A/EGFR/AXL/ITGA2/TFRC
## GO:0022414 ESR1/BCL2/AKT1/IGF1R/RB1/MTOR/MYH9/FOXO3/ATM/CASP8/PTEN/PARP1/CCNE2/AR/RAD51/ERCC1/CDKN1B/BCL2L11/KIT/EGFR/PTGS2/AXL/MSH2/CASP3/CCNE1/BCL2L1/MSH6/ITGA2/SMAD4/PIK3CA
## ID Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex 62 62/83
## GO:0044423 GO:0044423 virion component 0 0/83
## GO:0110165 GO:0110165 cellular anatomical entity 83 83/83
## geneID
## GO:0032991 ESR1/MET/BCL2/CCND1/NOTCH3/AKT1/IGF1R/RB1/CDKN1A/HSPA1A/MTOR/ETS1/ARID1A/MYH9/FOXO3/ATM/CASP8/PARP1/CCNE2/AR/EIF4E/MAPT/RAD51/ERCC1/PIK3R1/CHEK1/SRSF1/STAT5A/CDKN1B/BCL2L11/KIT/NCOA3/EGFR/EZH2/PTGS2/YBX1/PRKAA1/PXN/E2F1/CASP9/AXL/CDKN2A/MYC/MSH2/CASP3/CCNE1/YAP1/BCL2L1/DVL3/EIF4G1/FN1/GAPDH/MSH6/ITGA2/SMAD3/SMAD4/PIK3CA/PRKCA/TFRC/RAB11A/RICTOR/TP53BP1
## GO:0044423
## GO:0110165 ESR1/MET/G6PD/BCL2/KRAS/CCND1/NOTCH3/AKT1/IGF1R/RB1/XIAP/CDKN1A/HSPA1A/VHL/MTOR/MAPK8/ETS1/ARID1A/BID/MYH9/FOXO3/ATM/CASP8/MACC1/PTEN/NRAS/PTK2/PARP1/CCNE2/RAB25/AR/EIF4E/MAPT/RAD51/ERCC1/PIK3R1/CHEK1/SRSF1/TUBA1B/STAT5A/CDKN1B/BCL2L11/KIT/NCOA3/EGFR/EZH2/PTGS2/AKT2/YBX1/PRKAA1/PXN/E2F1/CASP9/AXL/CDKN2A/MYC/MSH2/CASP3/CCNE1/MAPK9/RAF1/YAP1/BCL2L1/DVL3/EIF4G1/FN1/GAPDH/MSH6/ITGA2/SMAD3/SMAD4/PIK3CA/PRKCA/MAPK1/MAPK3/TFRC/YWHAE/RAB11A/GAB2/ANLN/RICTOR/TP53BP1/BRAF
## ID Description Count GeneRatio
## GO:0003774 GO:0003774 cytoskeletal motor activity 0 0/19
## GO:0003824 GO:0003824 catalytic activity 10 10/19
## GO:0005198 GO:0005198 structural molecule activity 0 0/19
## GO:0005215 GO:0005215 transporter activity 0 0/19
## GO:0005488 GO:0005488 binding 19 19/19
## GO:0009055 GO:0009055 electron transfer activity 0 0/19
## geneID
## GO:0003774
## GO:0003824 G6PD/PTEN/ATM/EGFR/INPP4B/ACVRL1/CDK1/VHL/PRDX1/ERCC1
## GO:0005198
## GO:0005215
## GO:0005488 G6PD/IGFBP2/RBM15/PTEN/GATA3/PEA15/ATM/EGFR/INPP4B/ACVRL1/TSC1/PDCD4/CDK1/VHL/PRDX1/XBP1/ERCC1/TFRC/PREX1
## GO:0009055
## ID Description Count GeneRatio
## GO:0000003 GO:0000003 reproduction 7 7/19
## GO:0002376 GO:0002376 immune system process 11 11/19
## GO:0008152 GO:0008152 metabolic process 17 17/19
## GO:0009987 GO:0009987 cellular process 19 19/19
## GO:0016032 GO:0016032 viral process 3 3/19
## GO:0022414 GO:0022414 reproductive process 7 7/19
## geneID
## GO:0000003 IGFBP2/PTEN/GATA3/ATM/EGFR/CDK1/ERCC1
## GO:0002376 G6PD/IGFBP2/RBM15/GATA3/ATM/TSC1/PRDX1/XBP1/ERCC1/TFRC/PREX1
## GO:0008152 G6PD/RBM15/PTEN/GATA3/ATM/EGFR/INPP4B/ACVRL1/TSC1/PDCD4/CDK1/VHL/PRDX1/XBP1/ERCC1/TFRC/PREX1
## GO:0009987 G6PD/IGFBP2/RBM15/PTEN/GATA3/PEA15/ATM/EGFR/INPP4B/ACVRL1/TSC1/PDCD4/CDK1/VHL/PRDX1/XBP1/ERCC1/TFRC/PREX1
## GO:0016032 EGFR/CDK1/TFRC
## GO:0022414 IGFBP2/PTEN/GATA3/ATM/EGFR/CDK1/ERCC1
## ID Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex 11 11/19
## GO:0044423 GO:0044423 virion component 0 0/19
## GO:0110165 GO:0110165 cellular anatomical entity 19 19/19
## geneID
## GO:0032991 RBM15/GATA3/PEA15/ATM/EGFR/ACVRL1/TSC1/CDK1/XBP1/ERCC1/TFRC
## GO:0044423
## GO:0110165 G6PD/IGFBP2/RBM15/PTEN/GATA3/PEA15/ATM/EGFR/INPP4B/ACVRL1/TSC1/PDCD4/CDK1/VHL/PRDX1/XBP1/ERCC1/TFRC/PREX1
## ID Description Count GeneRatio
## GO:0003774 GO:0003774 cytoskeletal motor activity 0 0/55
## GO:0003824 GO:0003824 catalytic activity 29 29/55
## GO:0005198 GO:0005198 structural molecule activity 2 2/55
## GO:0005215 GO:0005215 transporter activity 2 2/55
## GO:0005488 GO:0005488 binding 55 55/55
## GO:0009055 GO:0009055 electron transfer activity 0 0/55
## geneID
## GO:0003774
## GO:0003824 MET/AKT2/G6PD/KRAS/CCND1/AKT1/IGF1R/XIAP/TUBA1B/MAPK8/PTEN/NRAS/PTK2/ATM/MAPK1/PIK3R1/CHEK1/CDKN1A/RAF1/PRKAA1/ACACA/NCOA3/CASP9/AXL/CCNE1/MAPK9/PRKCA/MAPK3/XRCC1
## GO:0005198 TUBA1B/FN1
## GO:0005215 BCL2/IGF1R
## GO:0005488 ESR1/MET/AKT2/G6PD/BCL2/KRAS/CCND1/NOTCH3/AKT1/IGF1R/MYC/BCL2L1/RB1/XIAP/TUBA1B/ETS1/MAPK8/ARID1A/BID/PTEN/NRAS/PTK2/ATM/YWHAZ/ITGA2/MAPK1/PXN/YWHAB/PIK3R1/CHEK1/SRSF1/CDKN1A/STAT5A/RAF1/PRKAA1/ACACA/NF2/NCOA3/E2F1/CASP9/AXL/CDKN2A/CCNE1/MAPK9/FOXO3/CTNNB1/DVL3/FN1/SMAD3/PRKCA/MAPK3/XRCC1/GAB2/WWTR1/TSC2
## GO:0009055
## ID Description Count GeneRatio
## GO:0000003 GO:0000003 reproduction 13 13/55
## GO:0002376 GO:0002376 immune system process 29 29/55
## GO:0008152 GO:0008152 metabolic process 50 50/55
## GO:0009987 GO:0009987 cellular process 55 55/55
## GO:0016032 GO:0016032 viral process 4 4/55
## GO:0022414 GO:0022414 reproductive process 13 13/55
## geneID
## GO:0000003 ESR1/BCL2/AKT1/IGF1R/BCL2L1/RB1/PTEN/ATM/ITGA2/AXL/CCNE1/FOXO3/CTNNB1
## GO:0002376 ESR1/G6PD/BCL2/AKT1/IGF1R/MYC/RB1/XIAP/ETS1/MAPK8/ARID1A/BID/PTK2/ATM/YWHAZ/ITGA2/MAPK1/PIK3R1/CDKN1A/RAF1/AXL/MAPK9/FOXO3/CTNNB1/FN1/SMAD3/PRKCA/MAPK3/GAB2
## GO:0008152 ESR1/MET/AKT2/G6PD/BCL2/KRAS/CCND1/NOTCH3/AKT1/IGF1R/MYC/RB1/XIAP/ETS1/MAPK8/ARID1A/BID/PTEN/PTK2/ATM/YWHAZ/ITGA2/MAPK1/YWHAB/PIK3R1/CHEK1/SRSF1/CDKN1A/STAT5A/RAF1/PRKAA1/ACACA/NF2/NCOA3/E2F1/CASP9/AXL/CDKN2A/CCNE1/MAPK9/FOXO3/CTNNB1/DVL3/FN1/SMAD3/PRKCA/MAPK3/XRCC1/WWTR1/TSC2
## GO:0009987 ESR1/MET/AKT2/G6PD/BCL2/KRAS/CCND1/NOTCH3/AKT1/IGF1R/MYC/BCL2L1/RB1/XIAP/TUBA1B/ETS1/MAPK8/ARID1A/BID/PTEN/NRAS/PTK2/ATM/YWHAZ/ITGA2/MAPK1/PXN/YWHAB/PIK3R1/CHEK1/SRSF1/CDKN1A/STAT5A/RAF1/PRKAA1/ACACA/NF2/NCOA3/E2F1/CASP9/AXL/CDKN2A/CCNE1/MAPK9/FOXO3/CTNNB1/DVL3/FN1/SMAD3/PRKCA/MAPK3/XRCC1/GAB2/WWTR1/TSC2
## GO:0016032 BCL2/AKT1/ITGA2/AXL
## GO:0022414 ESR1/BCL2/AKT1/IGF1R/BCL2L1/RB1/PTEN/ATM/ITGA2/AXL/CCNE1/FOXO3/CTNNB1
## ID Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex 36 36/55
## GO:0044423 GO:0044423 virion component 0 0/55
## GO:0110165 GO:0110165 cellular anatomical entity 55 55/55
## geneID
## GO:0032991 ESR1/MET/BCL2/CCND1/NOTCH3/AKT1/IGF1R/MYC/BCL2L1/RB1/ETS1/ARID1A/ATM/ITGA2/PXN/PIK3R1/CHEK1/SRSF1/CDKN1A/STAT5A/PRKAA1/NCOA3/E2F1/CASP9/AXL/CDKN2A/CCNE1/FOXO3/CTNNB1/DVL3/FN1/SMAD3/PRKCA/XRCC1/WWTR1/TSC2
## GO:0044423
## GO:0110165 ESR1/MET/AKT2/G6PD/BCL2/KRAS/CCND1/NOTCH3/AKT1/IGF1R/MYC/BCL2L1/RB1/XIAP/TUBA1B/ETS1/MAPK8/ARID1A/BID/PTEN/NRAS/PTK2/ATM/YWHAZ/ITGA2/MAPK1/PXN/YWHAB/PIK3R1/CHEK1/SRSF1/CDKN1A/STAT5A/RAF1/PRKAA1/ACACA/NF2/NCOA3/E2F1/CASP9/AXL/CDKN2A/CCNE1/MAPK9/FOXO3/CTNNB1/DVL3/FN1/SMAD3/PRKCA/MAPK3/XRCC1/GAB2/WWTR1/TSC2
## ID Description Count GeneRatio
## GO:0003774 GO:0003774 cytoskeletal motor activity 0 0/6
## GO:0003824 GO:0003824 catalytic activity 3 3/6
## GO:0005198 GO:0005198 structural molecule activity 0 0/6
## GO:0005215 GO:0005215 transporter activity 0 0/6
## GO:0005488 GO:0005488 binding 6 6/6
## GO:0009055 GO:0009055 electron transfer activity 0 0/6
## geneID
## GO:0003774
## GO:0003824 EGFR/GAPDH/ERCC1
## GO:0005198
## GO:0005215
## GO:0005488 IGFBP2/RBM15/EGFR/TSC1/GAPDH/ERCC1
## GO:0009055
## ID Description Count GeneRatio
## GO:0000003 GO:0000003 reproduction 3 3/6
## GO:0002376 GO:0002376 immune system process 5 5/6
## GO:0008152 GO:0008152 metabolic process 5 5/6
## GO:0009987 GO:0009987 cellular process 6 6/6
## GO:0016032 GO:0016032 viral process 1 1/6
## GO:0022414 GO:0022414 reproductive process 3 3/6
## geneID
## GO:0000003 IGFBP2/EGFR/ERCC1
## GO:0002376 IGFBP2/RBM15/TSC1/GAPDH/ERCC1
## GO:0008152 RBM15/EGFR/TSC1/GAPDH/ERCC1
## GO:0009987 IGFBP2/RBM15/EGFR/TSC1/GAPDH/ERCC1
## GO:0016032 EGFR
## GO:0022414 IGFBP2/EGFR/ERCC1
## ID Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex 5 5/6
## GO:0044423 GO:0044423 virion component 0 0/6
## GO:0110165 GO:0110165 cellular anatomical entity 6 6/6
## geneID
## GO:0032991 RBM15/EGFR/TSC1/GAPDH/ERCC1
## GO:0044423
## GO:0110165 IGFBP2/RBM15/EGFR/TSC1/GAPDH/ERCC1
## ID Description Count GeneRatio
## GO:0003774 GO:0003774 cytoskeletal motor activity 0 0/7
## GO:0003824 GO:0003824 catalytic activity 4 4/7
## GO:0005198 GO:0005198 structural molecule activity 0 0/7
## GO:0005215 GO:0005215 transporter activity 0 0/7
## GO:0005488 GO:0005488 binding 7 7/7
## GO:0009055 GO:0009055 electron transfer activity 0 0/7
## geneID
## GO:0003774
## GO:0003824 G6PD/ASNS/EGFR/GAPDH
## GO:0005198
## GO:0005215
## GO:0005488 G6PD/ASNS/RBM15/GATA3/EGFR/GAPDH/PREX1
## GO:0009055
## ID Description Count GeneRatio
## GO:0000003 GO:0000003 reproduction 2 2/7
## GO:0002376 GO:0002376 immune system process 5 5/7
## GO:0008152 GO:0008152 metabolic process 7 7/7
## GO:0009987 GO:0009987 cellular process 7 7/7
## GO:0016032 GO:0016032 viral process 1 1/7
## GO:0022414 GO:0022414 reproductive process 2 2/7
## geneID
## GO:0000003 GATA3/EGFR
## GO:0002376 G6PD/RBM15/GATA3/GAPDH/PREX1
## GO:0008152 G6PD/ASNS/RBM15/GATA3/EGFR/GAPDH/PREX1
## GO:0009987 G6PD/ASNS/RBM15/GATA3/EGFR/GAPDH/PREX1
## GO:0016032 EGFR
## GO:0022414 GATA3/EGFR
## ID Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex 4 4/7
## GO:0044423 GO:0044423 virion component 0 0/7
## GO:0110165 GO:0110165 cellular anatomical entity 7 7/7
## geneID
## GO:0032991 RBM15/GATA3/EGFR/GAPDH
## GO:0044423
## GO:0110165 G6PD/ASNS/RBM15/GATA3/EGFR/GAPDH/PREX1
## ID Description Count GeneRatio
## GO:0003774 GO:0003774 cytoskeletal motor activity 0 0/5
## GO:0003824 GO:0003824 catalytic activity 1 1/5
## GO:0005198 GO:0005198 structural molecule activity 0 0/5
## GO:0005215 GO:0005215 transporter activity 0 0/5
## GO:0005488 GO:0005488 binding 5 5/5
## GO:0009055 GO:0009055 electron transfer activity 0 0/5
## geneID
## GO:0003774
## GO:0003824 CDK1
## GO:0005198
## GO:0005215
## GO:0005488 ANLN/STMN1/CDK1/CCNB1/FOXM1
## GO:0009055
## ID Description Count GeneRatio
## GO:0000003 GO:0000003 reproduction 1 1/5
## GO:0002376 GO:0002376 immune system process 0 0/5
## GO:0008152 GO:0008152 metabolic process 3 3/5
## GO:0009987 GO:0009987 cellular process 5 5/5
## GO:0016032 GO:0016032 viral process 1 1/5
## GO:0022414 GO:0022414 reproductive process 1 1/5
## geneID
## GO:0000003 CDK1
## GO:0002376
## GO:0008152 CDK1/CCNB1/FOXM1
## GO:0009987 ANLN/STMN1/CDK1/CCNB1/FOXM1
## GO:0016032 CDK1
## GO:0022414 CDK1
## ID Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex 3 3/5
## GO:0044423 GO:0044423 virion component 0 0/5
## GO:0110165 GO:0110165 cellular anatomical entity 5 5/5
## geneID
## GO:0032991 CDK1/CCNB1/FOXM1
## GO:0044423
## GO:0110165 ANLN/STMN1/CDK1/CCNB1/FOXM1
## ID Description Count GeneRatio geneID
## GO:0003774 GO:0003774 cytoskeletal motor activity 0 0/0
## GO:0003824 GO:0003824 catalytic activity 0 0/0
## GO:0005198 GO:0005198 structural molecule activity 0 0/0
## GO:0005215 GO:0005215 transporter activity 0 0/0
## GO:0005488 GO:0005488 binding 0 0/0
## GO:0009055 GO:0009055 electron transfer activity 0 0/0
## ID Description Count GeneRatio geneID
## GO:0000003 GO:0000003 reproduction 0 0/0
## GO:0002376 GO:0002376 immune system process 0 0/0
## GO:0008152 GO:0008152 metabolic process 0 0/0
## GO:0009987 GO:0009987 cellular process 0 0/0
## GO:0016032 GO:0016032 viral process 0 0/0
## GO:0022414 GO:0022414 reproductive process 0 0/0
## ID Description Count GeneRatio geneID
## GO:0032991 GO:0032991 protein-containing complex 0 0/0
## GO:0044423 GO:0044423 virion component 0 0/0
## GO:0110165 GO:0110165 cellular anatomical entity 0 0/0
## ID Description Count GeneRatio geneID
## GO:0003774 GO:0003774 cytoskeletal motor activity 0 0/0
## GO:0003824 GO:0003824 catalytic activity 0 0/0
## GO:0005198 GO:0005198 structural molecule activity 0 0/0
## GO:0005215 GO:0005215 transporter activity 0 0/0
## GO:0005488 GO:0005488 binding 0 0/0
## GO:0009055 GO:0009055 electron transfer activity 0 0/0
## ID Description Count GeneRatio geneID
## GO:0000003 GO:0000003 reproduction 0 0/0
## GO:0002376 GO:0002376 immune system process 0 0/0
## GO:0008152 GO:0008152 metabolic process 0 0/0
## GO:0009987 GO:0009987 cellular process 0 0/0
## GO:0016032 GO:0016032 viral process 0 0/0
## GO:0022414 GO:0022414 reproductive process 0 0/0
## ID Description Count GeneRatio geneID
## GO:0032991 GO:0032991 protein-containing complex 0 0/0
## GO:0044423 GO:0044423 virion component 0 0/0
## GO:0110165 GO:0110165 cellular anatomical entity 0 0/0
## ID Description Count GeneRatio geneID
## GO:0003774 GO:0003774 cytoskeletal motor activity 0 0/0
## GO:0003824 GO:0003824 catalytic activity 0 0/0
## GO:0005198 GO:0005198 structural molecule activity 0 0/0
## GO:0005215 GO:0005215 transporter activity 0 0/0
## GO:0005488 GO:0005488 binding 0 0/0
## GO:0009055 GO:0009055 electron transfer activity 0 0/0
## ID Description Count GeneRatio geneID
## GO:0000003 GO:0000003 reproduction 0 0/0
## GO:0002376 GO:0002376 immune system process 0 0/0
## GO:0008152 GO:0008152 metabolic process 0 0/0
## GO:0009987 GO:0009987 cellular process 0 0/0
## GO:0016032 GO:0016032 viral process 0 0/0
## GO:0022414 GO:0022414 reproductive process 0 0/0
## ID Description Count GeneRatio geneID
## GO:0032991 GO:0032991 protein-containing complex 0 0/0
## GO:0044423 GO:0044423 virion component 0 0/0
## GO:0110165 GO:0110165 cellular anatomical entity 0 0/0barplot(ggo_MF[[1]], title = "groupGO, Molecular Function, Factor 1 of 1")
barplot(ggo_MF[[2]], title = "groupGO, Molecular Function, Factor 1 of 2")
barplot(ggo_MF[[3]], title = "groupGO, Molecular Function, Factor 2 of 2")
barplot(ggo_MF[[4]], title = "groupGO, Molecular Function, Factor 1 of 3")
barplot(ggo_MF[[5]], title = "groupGO, Molecular Function, Factor 2 of 3")
barplot(ggo_MF[[6]], title = "groupGO, Molecular Function, Factor 3 of 3")
barplot(ggo_MF[[7]], title = "groupGO, Molecular Function, Factor 1 of 5")
barplot(ggo_MF[[8]], title = "groupGO, Molecular Function, Factor 2 of 5")
barplot(ggo_MF[[9]], title = "groupGO, Molecular Function, Factor 3 of 5")
barplot(ggo_MF[[10]], title = "groupGO, Molecular Function, Factor 4 of 5")
barplot(ggo_MF[[11]], title = "groupGO, Molecular Function, Factor 5 of 5")
barplot(ggo_MF[[12]], title = "groupGO, Molecular Function, Factor 1 of 10")
barplot(ggo_MF[[13]], title = "groupGO, Molecular Function, Factor 2 of 10")
barplot(ggo_MF[[14]], title = "groupGO, Molecular Function, Factor 3 of 10")
barplot(ggo_MF[[15]], title = "groupGO, Molecular Function, Factor 4 of 10")
barplot(ggo_MF[[16]], title = "groupGO, Molecular Function, Factor 5 of 10")
barplot(ggo_MF[[17]], title = "groupGO, Molecular Function, Factor 6 of 10")
barplot(ggo_MF[[18]], title = "groupGO, Molecular Function, Factor 7 of 10")
barplot(ggo_MF[[19]], title = "groupGO, Molecular Function, Factor 8 of 10")
barplot(ggo_MF[[20]], title = "groupGO, Molecular Function, Factor 9 of 10")
barplot(ggo_MF[[21]], title = "groupGO, Molecular Function, Factor 10 of 10")
barplot(ggo_BP[[1]], title = "groupGO, Biological Process, Factor 1 of 1")
barplot(ggo_BP[[2]], title = "groupGO, Biological Process, Factor 1 of 2")
barplot(ggo_BP[[3]], title = "groupGO, Biological Process, Factor 2 of 2")
barplot(ggo_BP[[4]], title = "groupGO, Biological Process, Factor 1 of 3")
barplot(ggo_BP[[5]], title = "groupGO, Biological Process, Factor 2 of 3")
barplot(ggo_BP[[6]], title = "groupGO, Biological Process, Factor 3 of 3")
barplot(ggo_BP[[7]], title = "groupGO, Biological Process, Factor 1 of 5")
barplot(ggo_BP[[8]], title = "groupGO, Biological Process, Factor 2 of 5")
barplot(ggo_BP[[9]], title = "groupGO, Biological Process, Factor 3 of 5")
barplot(ggo_BP[[10]], title = "groupGO, Biological Process, Factor 4 of 5")
barplot(ggo_BP[[11]], title = "groupGO, Biological Process, Factor 5 of 5")
barplot(ggo_BP[[12]], title = "groupGO, Biological Process, Factor 1 of 10")
barplot(ggo_BP[[13]], title = "groupGO, Biological Process, Factor 2 of 10")
barplot(ggo_BP[[14]], title = "groupGO, Biological Process, Factor 3 of 10")
barplot(ggo_BP[[15]], title = "groupGO, Biological Process, Factor 4 of 10")
barplot(ggo_BP[[16]], title = "groupGO, Biological Process, Factor 5 of 10")
barplot(ggo_BP[[17]], title = "groupGO, Biological Process, Factor 6 of 10")
barplot(ggo_BP[[18]], title = "groupGO, Biological Process, Factor 7 of 10")
barplot(ggo_BP[[19]], title = "groupGO, Biological Process, Factor 8 of 10")
barplot(ggo_BP[[20]], title = "groupGO, Biological Process, Factor 9 of 10")
barplot(ggo_BP[[21]], title = "groupGO, Biological Process, Factor 10 of 10")
barplot(ggo_CC[[1]], title = "groupGO, Cellular Component, Factor 1 of 1")
barplot(ggo_CC[[2]], title = "groupGO, Cellular Component, Factor 1 of 2")
barplot(ggo_CC[[3]], title = "groupGO, Cellular Component, Factor 2 of 2")
barplot(ggo_CC[[4]], title = "groupGO, Cellular Component, Factor 1 of 3")
barplot(ggo_CC[[5]], title = "groupGO, Cellular Component, Factor 2 of 3")
barplot(ggo_CC[[6]], title = "groupGO, Cellular Component, Factor 3 of 3")
barplot(ggo_CC[[7]], title = "groupGO, Cellular Component, Factor 1 of 5")
barplot(ggo_CC[[8]], title = "groupGO, Cellular Component, Factor 2 of 5")
barplot(ggo_CC[[9]], title = "groupGO, Cellular Component, Factor 3 of 5")
barplot(ggo_CC[[10]], title = "groupGO, Cellular Component, Factor 4 of 5")
barplot(ggo_CC[[11]], title = "groupGO, Cellular Component, Factor 5 of 5")
barplot(ggo_CC[[12]], title = "groupGO, Cellular Component, Factor 1 of 10")
barplot(ggo_CC[[13]], title = "groupGO, Cellular Component, Factor 2 of 10")
barplot(ggo_CC[[14]], title = "groupGO, Cellular Component, Factor 3 of 10")
barplot(ggo_CC[[15]], title = "groupGO, Cellular Component, Factor 4 of 10")
barplot(ggo_CC[[16]], title = "groupGO, Cellular Component, Factor 5 of 10")
barplot(ggo_CC[[17]], title = "groupGO, Cellular Component, Factor 6 of 10")
barplot(ggo_CC[[18]], title = "groupGO, Cellular Component, Factor 7 of 10")
barplot(ggo_CC[[19]], title = "groupGO, Cellular Component, Factor 8 of 10")
barplot(ggo_CC[[20]], title = "groupGO, Cellular Component, Factor 9 of 10")
barplot(ggo_CC[[21]], title = "groupGO, Cellular Component, Factor 10 of 10")
B. GO Over-Representation
ego_MF <- list()#GO enrichment of a geneset for Molecular Function
ego_BP <- list()#GO enrichment of a geneset for Biological Process
ego_CC <- list()#GO enrichment of a geneset for Cellular Component
for(z in 1:length(geneNames)){
print(z)
input <- geneNames[[z]]
ego_MF[[z]] <- enrichGO(
gene = input,
OrgDb = org.Hs.eg.db,
ont = "MF",
pAdjustMethod = "BH",
keyType="SYMBOL",
pvalueCutoff = 0.05,
qvalueCutoff = 0.05,
minGSSize = 2,
readable = TRUE)
ego_BP[[z]] <- enrichGO(
gene = input,
OrgDb = org.Hs.eg.db,
ont = "BP",
pAdjustMethod = "BH",
keyType="SYMBOL",
pvalueCutoff = 0.05,
qvalueCutoff = 0.05,
minGSSize = 2,
readable = TRUE)
ego_CC[[z]] <- enrichGO(
gene = input,
OrgDb = org.Hs.eg.db,
ont = "CC",
pAdjustMethod = "BH",
keyType="SYMBOL",
pvalueCutoff = 0.05,
qvalueCutoff = 0.05,
minGSSize = 2,
readable = TRUE)
}## [1] 1
## [1] 2
## [1] 3
## [1] 4
## [1] 5
## [1] 6## --> No gene can be mapped....## --> Expected input gene ID: ALG12,PDSS2,RBBP8,GGT5,PIGM,RAD50## --> return NULL...## --> No gene can be mapped....## --> Expected input gene ID: FASTKD2,FST,SPATA22,ACTL9,SUN2,UBE2B## --> return NULL...## --> No gene can be mapped....## --> Expected input gene ID: KAT2B,MTA3,NRIP1,ZNF541,MECOM,SF3B3## --> return NULL...## [1] 7
## [1] 8
## [1] 9
## [1] 10## No gene sets have size between 2 and 500 ...
## --> return NULL...## [1] 11
## [1] 12
## [1] 13
## [1] 14
## [1] 15
## [1] 16
## [1] 17
## [1] 18
## [1] 19## --> No gene can be mapped....## --> Expected input gene ID: TMTC2,ALG1L2,PIGM,LCT,NDUFAB1,DPY19L4## --> return NULL...## --> No gene can be mapped....## --> Expected input gene ID: BRINP1,MAP10,SPIDR,TBATA,PTGFR,ACTL9## --> return NULL...## --> No gene can be mapped....## --> Expected input gene ID: POTEI,HDAC10,TAF1D,ACTB,ZNHIT1,KAT6A## --> return NULL...## [1] 20## --> No gene can be mapped....## --> Expected input gene ID: PDSS1,DPY19L2,GGT1,ALG3,NDUFAB1,DPY19L2P2## --> return NULL...## --> No gene can be mapped....## --> Expected input gene ID: RAD51D,DMRT1,ORC4,UBE2Q1,IL12B,BASP1## --> return NULL...## --> No gene can be mapped....## --> Expected input gene ID: HDAC11,ING4,CHD5,BRD8,ERCC1,TAF2## --> return NULL...## [1] 21## --> No gene can be mapped....## --> Expected input gene ID: ALG9,PDSS2,DPY19L2P2,DCLRE1C,TMEM260,ALG1## --> return NULL...## --> No gene can be mapped....## --> Expected input gene ID: ATP8B3,FANCA,NRIP1,NR3C1,PYGO2,NPY5R## --> return NULL...## --> No gene can be mapped....## --> Expected input gene ID: GATAD2B,BRPF3,HDAC6,TADA3,KAT2A,MBD3## --> return NULL...for(z in 1:18){ #19-21 don't work
#print(z)
print(head(ego_MF[[z]]))
print(head(ego_BP[[z]]))
print(head(ego_CC[[z]]))
}## ID Description
## GO:0004674 GO:0004674 protein serine/threonine kinase activity
## GO:0019902 GO:0019902 phosphatase binding
## GO:0106310 GO:0106310 protein serine kinase activity
## GO:0019903 GO:0019903 protein phosphatase binding
## GO:0035173 GO:0035173 histone kinase activity
## GO:0004714 GO:0004714 transmembrane receptor protein tyrosine kinase activity
## GeneRatio BgRatio pvalue p.adjust qvalue
## GO:0004674 11/52 427/18522 2.219321e-08 6.801858e-06 3.116409e-06
## GO:0019902 8/52 189/18522 5.195320e-08 6.801858e-06 3.116409e-06
## GO:0106310 10/52 363/18522 5.621370e-08 6.801858e-06 3.116409e-06
## GO:0019903 7/52 142/18522 1.345680e-07 1.221205e-05 5.595196e-06
## GO:0035173 4/52 23/18522 4.701052e-07 3.412964e-05 1.563718e-05
## GO:0004714 5/52 60/18522 6.958767e-07 4.117645e-05 1.886582e-05
## geneID Count
## GO:0004674 AKT1/MTOR/MAPK8/ATM/CHEK1/EGFR/AKT2/PRKAA1/PRKCA/MAPK1/BRAF 11
## GO:0019902 MAPK8/PTK2/PIK3R1/EGFR/MET/PXN/MAPK1/YWHAE 8
## GO:0106310 AKT1/MTOR/MAPK8/ATM/CHEK1/AKT2/PRKAA1/PRKCA/MAPK1/BRAF 10
## GO:0019903 MAPK8/PTK2/PIK3R1/EGFR/MET/PXN/YWHAE 7
## GO:0035173 ATM/CHEK1/PRKAA1/PRKCA 4
## GO:0004714 IGF1R/KIT/EGFR/MET/AXL 5
## ID Description GeneRatio
## GO:0071214 GO:0071214 cellular response to abiotic stimulus 16/52
## GO:0104004 GO:0104004 cellular response to environmental stimulus 16/52
## GO:0018105 GO:0018105 peptidyl-serine phosphorylation 15/52
## GO:0018209 GO:0018209 peptidyl-serine modification 15/52
## GO:0062197 GO:0062197 cellular response to chemical stress 15/52
## GO:0071496 GO:0071496 cellular response to external stimulus 15/52
## BgRatio pvalue p.adjust qvalue
## GO:0071214 334/18888 3.722278e-16 5.438247e-13 2.239244e-13
## GO:0104004 334/18888 3.722278e-16 5.438247e-13 2.239244e-13
## GO:0018105 282/18888 7.685832e-16 7.486000e-13 3.082423e-13
## GO:0018209 294/18888 1.426578e-15 1.042115e-12 4.290996e-13
## GO:0062197 311/18888 3.277191e-15 1.915191e-12 7.885957e-13
## GO:0071496 335/18888 9.798753e-15 4.771993e-12 1.964908e-12
## geneID
## GO:0071214 MTOR/MAPK8/CDKN1A/ATM/CASP8/PTEN/PIK3R1/CHEK1/IGF1R/EGFR/PTGS2/AKT2/CASP3/YAP1/ITGA2/TP53BP1
## GO:0104004 MTOR/MAPK8/CDKN1A/ATM/CASP8/PTEN/PIK3R1/CHEK1/IGF1R/EGFR/PTGS2/AKT2/CASP3/YAP1/ITGA2/TP53BP1
## GO:0018105 AKT1/MTOR/MAPK8/ATM/PTEN/EGFR/PTGS2/AKT2/PRKAA1/EIF4G1/PRKCA/MAPK1/TFRC/RICTOR/BRAF
## GO:0018209 AKT1/MTOR/MAPK8/ATM/PTEN/EGFR/PTGS2/AKT2/PRKAA1/EIF4G1/PRKCA/MAPK1/TFRC/RICTOR/BRAF
## GO:0062197 HSPA1A/AKT1/MTOR/MAPK8/FOXO3/ATM/EGFR/EZH2/PTGS2/MET/PRKAA1/PXN/AXL/CASP3/MAPK1
## GO:0071496 MTOR/MAPK8/CDKN1A/FOXO3/CASP8/CHEK1/IGF1R/EGFR/PTGS2/PRKAA1/AXL/EIF4G1/ITGA2/MAPK1/RICTOR
## Count
## GO:0071214 16
## GO:0104004 16
## GO:0018105 15
## GO:0018209 15
## GO:0062197 15
## GO:0071496 15
## ID
## GO:0005925 GO:0005925
## GO:0030055 GO:0030055
## GO:0005826 GO:0005826
## GO:1902911 GO:1902911
## GO:0000781 GO:0000781
## GO:0061695 GO:0061695
## Description
## GO:0005925 focal adhesion
## GO:0030055 cell-substrate junction
## GO:0005826 actomyosin contractile ring
## GO:1902911 protein kinase complex
## GO:0000781 chromosome, telomeric region
## GO:0061695 transferase complex, transferring phosphorus-containing groups
## GeneRatio BgRatio pvalue p.adjust qvalue
## GO:0005925 9/52 421/19894 1.284721e-06 0.0001691692 9.026737e-05
## GO:0030055 9/52 431/19894 1.559164e-06 0.0001691692 9.026737e-05
## GO:0005826 2/52 4/19894 4.007244e-05 0.0024155554 1.288921e-03
## GO:1902911 5/52 150/19894 4.452637e-05 0.0024155554 1.288921e-03
## GO:0000781 5/52 173/19894 8.763402e-05 0.0038033166 2.029420e-03
## GO:0061695 6/52 308/19894 1.467139e-04 0.0046290010 2.469998e-03
## geneID Count
## GO:0005925 HSPA1A/MYH9/KRAS/PTK2/EGFR/PXN/ITGA2/MAPK1/YWHAE 9
## GO:0030055 HSPA1A/MYH9/KRAS/PTK2/EGFR/PXN/ITGA2/MAPK1/YWHAE 9
## GO:0005826 MYH9/ANLN 2
## GO:1902911 CDKN1A/CCND1/IGF1R/PRKAA1/CCNE1 5
## GO:0000781 ATM/CHEK1/EZH2/MSH2/TP53BP1 5
## GO:0061695 CDKN1A/CCND1/PIK3R1/IGF1R/PRKAA1/CCNE1 6
## ID Description GeneRatio
## GO:0032143 GO:0032143 single thymine insertion binding 2/18
## GO:0032137 GO:0032137 guanine/thymine mispair binding 2/18
## GO:0032142 GO:0032142 single guanine insertion binding 2/18
## GO:0032138 GO:0032138 single base insertion or deletion binding 2/18
## GO:0032135 GO:0032135 DNA insertion or deletion binding 2/18
## GO:0032405 GO:0032405 MutLalpha complex binding 2/18
## BgRatio pvalue p.adjust qvalue geneID Count
## GO:0032143 2/18522 8.920088e-07 0.0001239178 5.442812e-05 MSH6/MSH2 2
## GO:0032137 3/18522 2.674485e-06 0.0001239178 5.442812e-05 MSH6/MSH2 2
## GO:0032142 3/18522 2.674485e-06 0.0001239178 5.442812e-05 MSH6/MSH2 2
## GO:0032138 4/18522 5.345889e-06 0.0001857697 8.159515e-05 MSH6/MSH2 2
## GO:0032135 6/18522 1.334933e-05 0.0003092596 1.358353e-04 MSH6/MSH2 2
## GO:0032405 6/18522 1.334933e-05 0.0003092596 1.358353e-04 MSH6/MSH2 2
## ID
## GO:0002562 GO:0002562
## GO:0016444 GO:0016444
## GO:0002200 GO:0002200
## GO:0002520 GO:0002520
## GO:0002312 GO:0002312
## GO:0002285 GO:0002285
## Description
## GO:0002562 somatic diversification of immune receptors via germline recombination within a single locus
## GO:0016444 somatic cell DNA recombination
## GO:0002200 somatic diversification of immune receptors
## GO:0002520 immune system development
## GO:0002312 B cell activation involved in immune response
## GO:0002285 lymphocyte activation involved in immune response
## GeneRatio BgRatio pvalue p.adjust qvalue
## GO:0002562 4/18 70/18888 5.088977e-07 0.0002509906 0.0001319869
## GO:0016444 4/18 70/18888 5.088977e-07 0.0002509906 0.0001319869
## GO:0002200 4/18 76/18888 7.095469e-07 0.0002509906 0.0001319869
## GO:0002520 5/18 197/18888 9.001426e-07 0.0002509906 0.0001319869
## GO:0002312 4/18 87/18888 1.223008e-06 0.0002509906 0.0001319869
## GO:0002285 5/18 212/18888 1.292655e-06 0.0002509906 0.0001319869
## geneID Count
## GO:0002562 ATM/MSH6/TFRC/MSH2 4
## GO:0016444 ATM/MSH6/TFRC/MSH2 4
## GO:0002200 ATM/MSH6/TFRC/MSH2 4
## GO:0002520 RBM15/ATM/MSH6/TFRC/MSH2 5
## GO:0002312 XBP1/MSH6/TFRC/MSH2 4
## GO:0002285 TSC1/XBP1/MSH6/TFRC/MSH2 5
## ID Description GeneRatio BgRatio pvalue
## GO:0032301 GO:0032301 MutSalpha complex 2/18 2/19894 7.732128e-07
## GO:0032300 GO:0032300 mismatch repair complex 2/18 11/19894 4.232193e-05
## GO:0042470 GO:0042470 melanosome 3/18 112/19894 1.332719e-04
## GO:0048770 GO:0048770 pigment granule 3/18 112/19894 1.332719e-04
## GO:0032302 GO:0032302 MutSbeta complex 1/18 2/19894 1.808818e-03
## GO:0061793 GO:0061793 chromatin lock complex 1/18 3/19894 2.712067e-03
## p.adjust qvalue geneID Count
## GO:0032301 7.345522e-05 5.209012e-05 MSH6/MSH2 2
## GO:0032300 2.010292e-03 1.425581e-03 MSH6/MSH2 2
## GO:0042470 3.165208e-03 2.244580e-03 FASN/PRDX1/TFRC 3
## GO:0048770 3.165208e-03 2.244580e-03 FASN/PRDX1/TFRC 3
## GO:0032302 3.436753e-02 2.437144e-02 MSH2 1
## GO:0061793 4.292272e-02 3.043827e-02 RB1 1
## ID Description GeneRatio
## GO:0019902 GO:0019902 phosphatase binding 9/60
## GO:0004674 GO:0004674 protein serine/threonine kinase activity 12/60
## GO:0019207 GO:0019207 kinase regulator activity 10/60
## GO:0019903 GO:0019903 protein phosphatase binding 8/60
## GO:0106310 GO:0106310 protein serine kinase activity 11/60
## GO:0019887 GO:0019887 protein kinase regulator activity 9/60
## BgRatio pvalue p.adjust qvalue
## GO:0019902 189/18522 9.356678e-09 1.578662e-06 7.619938e-07
## GO:0004674 427/18522 9.942813e-09 1.578662e-06 7.619938e-07
## GO:0019207 270/18522 1.456427e-08 1.578662e-06 7.619938e-07
## GO:0019903 142/18522 1.789157e-08 1.578662e-06 7.619938e-07
## GO:0106310 363/18522 2.044899e-08 1.578662e-06 7.619938e-07
## GO:0019887 232/18522 5.515042e-08 3.548010e-06 1.712566e-06
## geneID
## GO:0019902 MAPK8/PTK2/PIK3R1/EGFR/MET/PXN/BCL2/MAPK1/YWHAE
## GO:0004674 AKT1/MTOR/MAPK8/ATM/CHEK1/EGFR/AKT2/PRKAA1/PIK3CA/PRKCA/MAPK1/BRAF
## GO:0019207 AKT1/CDKN1A/CCNE2/CCND1/PIK3R1/EGFR/CASP3/CCNE1/PIK3CA/RICTOR
## GO:0019903 MAPK8/PTK2/PIK3R1/EGFR/MET/PXN/BCL2/YWHAE
## GO:0106310 AKT1/MTOR/MAPK8/ATM/CHEK1/AKT2/PRKAA1/PIK3CA/PRKCA/MAPK1/BRAF
## GO:0019887 AKT1/CDKN1A/CCNE2/CCND1/EGFR/CASP3/CCNE1/PIK3CA/RICTOR
## Count
## GO:0019902 9
## GO:0004674 12
## GO:0019207 10
## GO:0019903 8
## GO:0106310 11
## GO:0019887 9
## ID Description GeneRatio
## GO:0071214 GO:0071214 cellular response to abiotic stimulus 19/60
## GO:0104004 GO:0104004 cellular response to environmental stimulus 19/60
## GO:0009314 GO:0009314 response to radiation 20/60
## GO:0062197 GO:0062197 cellular response to chemical stress 17/60
## GO:0009416 GO:0009416 response to light stimulus 17/60
## GO:0018105 GO:0018105 peptidyl-serine phosphorylation 16/60
## BgRatio pvalue p.adjust qvalue
## GO:0071214 334/18888 3.213319e-19 5.107571e-16 2.039612e-16
## GO:0104004 334/18888 3.213319e-19 5.107571e-16 2.039612e-16
## GO:0009314 431/18888 1.713984e-18 1.816252e-15 7.252859e-16
## GO:0062197 311/18888 6.348179e-17 5.045215e-14 2.014712e-14
## GO:0009416 321/18888 1.078848e-16 6.859316e-14 2.739139e-14
## GO:0018105 282/18888 3.305462e-16 1.751344e-13 6.993661e-14
## geneID
## GO:0071214 MTOR/MAPK8/CDKN1A/ATM/CASP8/PTEN/PARP1/IGF1R/PIK3R1/CHEK1/EGFR/PTGS2/AKT2/MYC/CASP3/YAP1/ITGA2/PIK3CA/TP53BP1
## GO:0104004 MTOR/MAPK8/CDKN1A/ATM/CASP8/PTEN/PARP1/IGF1R/PIK3R1/CHEK1/EGFR/PTGS2/AKT2/MYC/CASP3/YAP1/ITGA2/PIK3CA/TP53BP1
## GO:0009314 AKT1/MAPK8/CDKN1A/ATM/KRAS/PARP1/CCND1/PIK3R1/KIT/EGFR/AKT2/PRKAA1/BCL2/MYC/MSH2/CASP3/YAP1/MSH6/TP53BP1/BRAF
## GO:0062197 HSPA1A/AKT1/MTOR/MAPK8/FOXO3/ATM/PARP1/EGFR/EZH2/PTGS2/MET/PRKAA1/PXN/AXL/CASP3/PIK3CA/MAPK1
## GO:0009416 AKT1/MAPK8/CDKN1A/KRAS/PARP1/CCND1/PIK3R1/KIT/EGFR/AKT2/PRKAA1/BCL2/MYC/MSH2/CASP3/MSH6/BRAF
## GO:0018105 AKT1/MTOR/MAPK8/ATM/PTEN/EGFR/PTGS2/AKT2/PRKAA1/BCL2/EIF4G1/PRKCA/MAPK1/TFRC/RICTOR/BRAF
## Count
## GO:0071214 19
## GO:0104004 19
## GO:0009314 20
## GO:0062197 17
## GO:0009416 17
## GO:0018105 16
## ID
## GO:0061695 GO:0061695
## GO:0005925 GO:0005925
## GO:0030055 GO:0030055
## GO:1902911 GO:1902911
## GO:0032301 GO:0032301
## GO:0031968 GO:0031968
## Description
## GO:0061695 transferase complex, transferring phosphorus-containing groups
## GO:0005925 focal adhesion
## GO:0030055 cell-substrate junction
## GO:1902911 protein kinase complex
## GO:0032301 MutSalpha complex
## GO:0031968 organelle outer membrane
## GeneRatio BgRatio pvalue p.adjust qvalue
## GO:0061695 8/60 308/19894 3.833410e-06 0.0003217012 0.000167818
## GO:0005925 9/60 421/19894 4.445599e-06 0.0003217012 0.000167818
## GO:0030055 9/60 431/19894 5.375758e-06 0.0003217012 0.000167818
## GO:1902911 6/60 150/19894 5.948983e-06 0.0003217012 0.000167818
## GO:0032301 2/60 2/19894 8.945011e-06 0.0003217012 0.000167818
## GO:0031968 7/60 248/19894 9.457031e-06 0.0003217012 0.000167818
## geneID Count
## GO:0061695 CDKN1A/IGF1R/CCNE2/CCND1/PIK3R1/PRKAA1/CCNE1/PIK3CA 8
## GO:0005925 HSPA1A/MYH9/KRAS/PTK2/EGFR/PXN/ITGA2/MAPK1/YWHAE 9
## GO:0030055 HSPA1A/MYH9/KRAS/PTK2/EGFR/PXN/ITGA2/MAPK1/YWHAE 9
## GO:1902911 CDKN1A/IGF1R/CCNE2/CCND1/PRKAA1/CCNE1 6
## GO:0032301 MSH2/MSH6 2
## GO:0031968 MTOR/FOXO3/CASP8/KRAS/PTGS2/BCL2/BCL2L11 7
## ID Description GeneRatio
## GO:0019902 GO:0019902 phosphatase binding 9/68
## GO:0004674 GO:0004674 protein serine/threonine kinase activity 12/68
## GO:0019903 GO:0019903 protein phosphatase binding 8/68
## GO:0019207 GO:0019207 kinase regulator activity 10/68
## GO:0106310 GO:0106310 protein serine kinase activity 11/68
## GO:0140297 GO:0140297 DNA-binding transcription factor binding 12/68
## BgRatio pvalue p.adjust qvalue
## GO:0019902 189/18522 2.907790e-08 5.335868e-06 2.348076e-06
## GO:0004674 427/18522 4.380221e-08 5.335868e-06 2.348076e-06
## GO:0019903 142/18522 4.909353e-08 5.335868e-06 2.348076e-06
## GO:0019207 270/18522 5.069709e-08 5.335868e-06 2.348076e-06
## GO:0106310 363/18522 7.952219e-08 6.695769e-06 2.946507e-06
## GO:0140297 478/18522 1.492674e-07 8.869803e-06 3.903201e-06
## geneID
## GO:0019902 MAPK8/PTK2/PIK3R1/EGFR/MET/PXN/BCL2/MAPK1/YWHAE
## GO:0004674 AKT1/MTOR/MAPK8/ATM/CHEK1/EGFR/AKT2/PRKAA1/PIK3CA/PRKCA/MAPK1/BRAF
## GO:0019903 MAPK8/PTK2/PIK3R1/EGFR/MET/PXN/BCL2/YWHAE
## GO:0019207 AKT1/CDKN1A/CCNE2/CCND1/PIK3R1/EGFR/CASP3/CCNE1/PIK3CA/RICTOR
## GO:0106310 AKT1/MTOR/MAPK8/ATM/CHEK1/AKT2/PRKAA1/PIK3CA/PRKCA/MAPK1/BRAF
## GO:0140297 RB1/VHL/ETS1/ARID1A/PARP1/STAT5A/NCOA3/BCL2/MYC/YAP1/EIF4E/TP53BP1
## Count
## GO:0019902 9
## GO:0004674 12
## GO:0019903 8
## GO:0019207 10
## GO:0106310 11
## GO:0140297 12
## ID Description GeneRatio
## GO:0051402 GO:0051402 neuron apoptotic process 19/68
## GO:0062197 GO:0062197 cellular response to chemical stress 19/68
## GO:0071214 GO:0071214 cellular response to abiotic stimulus 19/68
## GO:0104004 GO:0104004 cellular response to environmental stimulus 19/68
## GO:0009314 GO:0009314 response to radiation 20/68
## GO:0000082 GO:0000082 G1/S transition of mitotic cell cycle 16/68
## BgRatio pvalue p.adjust qvalue
## GO:0051402 292/18888 3.710445e-19 1.225189e-15 5.077451e-16
## GO:0062197 311/18888 1.216651e-18 2.008690e-15 8.324451e-16
## GO:0071214 334/18888 4.634435e-18 3.825726e-15 1.585465e-15
## GO:0104004 334/18888 4.634435e-18 3.825726e-15 1.585465e-15
## GO:0009314 431/18888 2.839156e-17 1.874978e-14 7.770321e-15
## GO:0000082 234/18888 1.526461e-16 8.400623e-14 3.481402e-14
## geneID
## GO:0051402 RB1/XIAP/BID/FOXO3/ATM/CASP8/KRAS/PARP1/CCND1/AKT2/BCL2/AXL/MSH2/CASP3/BCL2L11/GAPDH/PIK3CA/BRAF/G6PD
## GO:0062197 HSPA1A/AKT1/MTOR/MAPK8/FOXO3/ATM/PARP1/EGFR/EZH2/PTGS2/MET/PRKAA1/PXN/AXL/CASP3/PIK3CA/MAPK1/G6PD/PRDX1
## GO:0071214 MTOR/MAPK8/CDKN1A/ATM/CASP8/PTEN/PARP1/IGF1R/PIK3R1/CHEK1/EGFR/PTGS2/AKT2/MYC/CASP3/YAP1/ITGA2/PIK3CA/TP53BP1
## GO:0104004 MTOR/MAPK8/CDKN1A/ATM/CASP8/PTEN/PARP1/IGF1R/PIK3R1/CHEK1/EGFR/PTGS2/AKT2/MYC/CASP3/YAP1/ITGA2/PIK3CA/TP53BP1
## GO:0009314 AKT1/MAPK8/CDKN1A/ATM/KRAS/PARP1/CCND1/PIK3R1/KIT/EGFR/AKT2/PRKAA1/BCL2/MYC/MSH2/CASP3/YAP1/MSH6/TP53BP1/BRAF
## GO:0000082 RB1/AKT1/ARID1A/BID/CDKN1A/ATM/PTEN/CCNE2/CCND1/EGFR/EZH2/BCL2/MYC/CCNE1/EIF4E/EIF4G1
## Count
## GO:0051402 19
## GO:0062197 19
## GO:0071214 19
## GO:0104004 19
## GO:0009314 20
## GO:0000082 16
## ID
## GO:1902911 GO:1902911
## GO:0061695 GO:0061695
## GO:0000307 GO:0000307
## GO:0031968 GO:0031968
## GO:0019867 GO:0019867
## GO:0005741 GO:0005741
## Description
## GO:1902911 protein kinase complex
## GO:0061695 transferase complex, transferring phosphorus-containing groups
## GO:0000307 cyclin-dependent protein kinase holoenzyme complex
## GO:0031968 organelle outer membrane
## GO:0019867 outer membrane
## GO:0005741 mitochondrial outer membrane
## GeneRatio BgRatio pvalue p.adjust qvalue
## GO:1902911 7/68 150/19894 7.942399e-07 0.0001029510 5.644241e-05
## GO:0061695 9/68 308/19894 1.005924e-06 0.0001029510 5.644241e-05
## GO:0000307 5/68 56/19894 1.340841e-06 0.0001029510 5.644241e-05
## GO:0031968 8/68 248/19894 2.020319e-06 0.0001029510 5.644241e-05
## GO:0019867 8/68 250/19894 2.144812e-06 0.0001029510 5.644241e-05
## GO:0005741 7/68 219/19894 9.761782e-06 0.0003829512 2.099513e-04
## geneID Count
## GO:1902911 RB1/CDKN1A/IGF1R/CCNE2/CCND1/PRKAA1/CCNE1 7
## GO:0061695 RB1/CDKN1A/IGF1R/CCNE2/CCND1/PIK3R1/PRKAA1/CCNE1/PIK3CA 9
## GO:0000307 RB1/CDKN1A/CCNE2/CCND1/CCNE1 5
## GO:0031968 MTOR/BID/FOXO3/CASP8/KRAS/PTGS2/BCL2/BCL2L11 8
## GO:0019867 MTOR/BID/FOXO3/CASP8/KRAS/PTGS2/BCL2/BCL2L11 8
## GO:0005741 MTOR/BID/FOXO3/CASP8/KRAS/BCL2/BCL2L11 7
## ID Description GeneRatio
## GO:0140297 GO:0140297 DNA-binding transcription factor binding 8/28
## GO:0051434 GO:0051434 BH3 domain binding 2/28
## GO:0120283 GO:0120283 protein serine/threonine kinase binding 2/28
## GO:0051400 GO:0051400 BH domain binding 2/28
## GO:0031625 GO:0031625 ubiquitin protein ligase binding 5/28
## GO:0044389 GO:0044389 ubiquitin-like protein ligase binding 5/28
## BgRatio pvalue p.adjust qvalue
## GO:0140297 478/18522 3.662033e-07 6.481798e-05 3.315103e-05
## GO:0051434 6/18522 3.293323e-05 2.717739e-03 1.389983e-03
## GO:0120283 7/18522 4.606338e-05 2.717739e-03 1.389983e-03
## GO:0051400 9/18522 7.881811e-05 2.986797e-03 1.527592e-03
## GO:0031625 305/18522 8.437280e-05 2.986797e-03 1.527592e-03
## GO:0044389 324/18522 1.121207e-04 3.039125e-03 1.554355e-03
## geneID Count
## GO:0140297 BCL2/MYC/RB1/ETS1/ARID1A/YWHAZ/NCOA3/VHL 8
## GO:0051434 BCL2/BCL2L1 2
## GO:0120283 XIAP/MAPK8 2
## GO:0051400 BCL2/BCL2L1 2
## GO:0031625 BCL2/RB1/BID/YWHAZ/CDKN1A 5
## GO:0044389 BCL2/RB1/BID/YWHAZ/CDKN1A 5
## ID Description
## GO:0000082 GO:0000082 G1/S transition of mitotic cell cycle
## GO:0044843 GO:0044843 cell cycle G1/S phase transition
## GO:2000045 GO:2000045 regulation of G1/S transition of mitotic cell cycle
## GO:1902806 GO:1902806 regulation of cell cycle G1/S phase transition
## GO:0051402 GO:0051402 neuron apoptotic process
## GO:0009314 GO:0009314 response to radiation
## GeneRatio BgRatio pvalue p.adjust qvalue
## GO:0000082 10/28 234/18888 7.584848e-13 1.480562e-09 6.187639e-10
## GO:0044843 10/28 262/18888 2.340523e-12 2.284351e-09 9.546871e-10
## GO:2000045 9/28 185/18888 4.014629e-12 2.612185e-09 1.091697e-09
## GO:1902806 9/28 211/18888 1.312373e-11 6.404380e-09 2.676550e-09
## GO:0051402 9/28 292/18888 2.381356e-10 9.296814e-08 3.885370e-08
## GO:0009314 10/28 431/18888 3.135912e-10 1.020217e-07 4.263740e-08
## geneID Count
## GO:0000082 BCL2/MYC/AKT1/RB1/ARID1A/BID/PTEN/ATM/CCND1/CDKN1A 10
## GO:0044843 BCL2/MYC/AKT1/RB1/ARID1A/BID/PTEN/ATM/CCND1/CDKN1A 10
## GO:2000045 BCL2/AKT1/RB1/ARID1A/BID/PTEN/ATM/CCND1/CDKN1A 9
## GO:1902806 BCL2/AKT1/RB1/ARID1A/BID/PTEN/ATM/CCND1/CDKN1A 9
## GO:0051402 AKT2/BCL2/BCL2L1/RB1/XIAP/BID/KRAS/ATM/CCND1 9
## GO:0009314 AKT2/BCL2/MYC/AKT1/BCL2L1/MAPK8/KRAS/ATM/CCND1/CDKN1A 10
## ID Description
## GO:0005938 GO:0005938 cell cortex
## GO:0000307 GO:0000307 cyclin-dependent protein kinase holoenzyme complex
## GO:0097136 GO:0097136 Bcl-2 family protein complex
## GO:0005741 GO:0005741 mitochondrial outer membrane
## GO:0031968 GO:0031968 organelle outer membrane
## GO:0019867 GO:0019867 outer membrane
## GeneRatio BgRatio pvalue p.adjust qvalue
## GO:0005938 5/28 309/19894 6.414545e-05 0.003499998 0.001946939
## GO:0000307 3/28 56/19894 6.584049e-05 0.003499998 0.001946939
## GO:0097136 2/28 10/19894 8.536580e-05 0.003499998 0.001946939
## GO:0005741 4/28 219/19894 2.377369e-04 0.007310409 0.004066552
## GO:0031968 4/28 248/19894 3.813894e-04 0.008059755 0.004483389
## GO:0019867 4/28 250/19894 3.931588e-04 0.008059755 0.004483389
## geneID Count
## GO:0005938 AKT2/AKT1/PTK2/NF2/TSC1 5
## GO:0000307 RB1/CCND1/CDKN1A 3
## GO:0097136 BCL2/BCL2L1 2
## GO:0005741 BCL2/BCL2L1/BID/KRAS 4
## GO:0031968 BCL2/BCL2L1/BID/KRAS 4
## GO:0019867 BCL2/BCL2L1/BID/KRAS 4
## NULL
## NULL
## NULL
## ID Description GeneRatio
## GO:0032143 GO:0032143 single thymine insertion binding 2/22
## GO:0032137 GO:0032137 guanine/thymine mispair binding 2/22
## GO:0032142 GO:0032142 single guanine insertion binding 2/22
## GO:0032138 GO:0032138 single base insertion or deletion binding 2/22
## GO:0032135 GO:0032135 DNA insertion or deletion binding 2/22
## GO:0032405 GO:0032405 MutLalpha complex binding 2/22
## BgRatio pvalue p.adjust qvalue geneID Count
## GO:0032143 2/18522 1.346758e-06 0.0002314757 0.0001019966 MSH6/MSH2 2
## GO:0032137 3/18522 4.037366e-06 0.0002314757 0.0001019966 MSH6/MSH2 2
## GO:0032142 3/18522 4.037366e-06 0.0002314757 0.0001019966 MSH6/MSH2 2
## GO:0032138 4/18522 8.068919e-06 0.0003469635 0.0001528848 MSH6/MSH2 2
## GO:0032135 6/18522 2.014327e-05 0.0005774403 0.0002544413 MSH6/MSH2 2
## GO:0032405 6/18522 2.014327e-05 0.0005774403 0.0002544413 MSH6/MSH2 2
## ID Description
## GO:0010165 GO:0010165 response to X-ray
## GO:0002520 GO:0002520 immune system development
## GO:0002285 GO:0002285 lymphocyte activation involved in immune response
## GO:0051053 GO:0051053 negative regulation of DNA metabolic process
## GO:1903131 GO:1903131 mononuclear cell differentiation
## GO:0045785 GO:0045785 positive regulation of cell adhesion
## GeneRatio BgRatio pvalue p.adjust qvalue
## GO:0010165 4/22 28/18888 2.773903e-08 3.925073e-05 1.997210e-05
## GO:0002520 6/22 197/18888 7.744845e-08 5.479478e-05 2.788144e-05
## GO:0002285 6/22 212/18888 1.196329e-07 5.642687e-05 2.871190e-05
## GO:0051053 5/22 142/18888 5.316425e-07 1.702242e-04 8.661587e-05
## GO:1903131 7/22 484/18888 8.486227e-07 1.702242e-04 8.661587e-05
## GO:0045785 7/22 485/18888 8.604413e-07 1.702242e-04 8.661587e-05
## geneID Count
## GO:0010165 GATA3/ATM/BRCA2/MSH2 4
## GO:0002520 RBM15/GATA3/ATM/MSH6/TFRC/MSH2 6
## GO:0002285 GATA3/TSC1/XBP1/MSH6/TFRC/MSH2 6
## GO:0051053 GATA3/ATM/TTF1/MSH6/MSH2 5
## GO:1903131 GATA3/ATM/FASN/TSC1/XBP1/MSH2/PREX1 7
## GO:0045785 IGFBP2/GATA3/ATM/TSC1/XBP1/TFRC/PREX1 7
## ID Description GeneRatio BgRatio
## GO:0032301 GO:0032301 MutSalpha complex 2/22 2/19894
## GO:0097125 GO:0097125 cyclin B1-CDK1 complex 2/22 2/19894
## GO:0042470 GO:0042470 melanosome 4/22 112/19894
## GO:0048770 GO:0048770 pigment granule 4/22 112/19894
## GO:0000781 GO:0000781 chromosome, telomeric region 4/22 173/19894
## GO:0032300 GO:0032300 mismatch repair complex 2/22 11/19894
## pvalue p.adjust qvalue geneID Count
## GO:0032301 1.167400e-06 5.486779e-05 3.747967e-05 MSH6/MSH2 2
## GO:0097125 1.167400e-06 5.486779e-05 3.747967e-05 CDK1/CCNB1 2
## GO:0042470 6.439119e-06 1.513193e-04 1.033648e-04 FASN/PRDX1/MYH11/TFRC 4
## GO:0048770 6.439119e-06 1.513193e-04 1.033648e-04 FASN/PRDX1/MYH11/TFRC 4
## GO:0000781 3.574947e-05 6.720901e-04 4.590985e-04 CDK1/ATM/BRCA2/MSH2 4
## GO:0032300 6.382076e-05 8.750800e-04 5.977590e-04 MSH6/MSH2 2
## ID Description GeneRatio
## GO:0140297 GO:0140297 DNA-binding transcription factor binding 16/73
## GO:0004674 GO:0004674 protein serine/threonine kinase activity 15/73
## GO:0106310 GO:0106310 protein serine kinase activity 14/73
## GO:0019902 GO:0019902 phosphatase binding 11/73
## GO:0019207 GO:0019207 kinase regulator activity 11/73
## GO:0019887 GO:0019887 protein kinase regulator activity 10/73
## BgRatio pvalue p.adjust qvalue
## GO:0140297 478/18522 4.115363e-11 1.650260e-08 7.754210e-09
## GO:0004674 427/18522 9.278499e-11 1.668472e-08 7.839783e-09
## GO:0106310 363/18522 1.248234e-10 1.668472e-08 7.839783e-09
## GO:0019902 189/18522 1.914199e-10 1.918985e-08 9.016887e-09
## GO:0019207 270/18522 8.246097e-09 6.613370e-07 3.107477e-07
## GO:0019887 232/18522 2.440438e-08 1.631026e-06 7.663830e-07
## geneID
## GO:0140297 RB1/VHL/ETS1/ARID1A/PARP1/STAT5A/NCOA3/BCL2/E2F1/CDKN2A/MYC/YAP1/EIF4E/SMAD3/MAPK3/TP53BP1
## GO:0004674 AKT1/MTOR/MAPK8/ATM/CHEK1/EGFR/AKT2/PRKAA1/MAPK9/RAF1/PIK3CA/PRKCA/MAPK1/MAPK3/BRAF
## GO:0106310 AKT1/MTOR/MAPK8/ATM/CHEK1/AKT2/PRKAA1/MAPK9/RAF1/PIK3CA/PRKCA/MAPK1/MAPK3/BRAF
## GO:0019902 MAPK8/PTK2/PIK3R1/EGFR/MET/PXN/BCL2/SMAD3/MAPK1/MAPK3/YWHAE
## GO:0019207 AKT1/CDKN1A/CCNE2/CCND1/PIK3R1/EGFR/CDKN2A/CASP3/CCNE1/PIK3CA/RICTOR
## GO:0019887 AKT1/CDKN1A/CCNE2/CCND1/EGFR/CDKN2A/CASP3/CCNE1/PIK3CA/RICTOR
## Count
## GO:0140297 16
## GO:0004674 15
## GO:0106310 14
## GO:0019902 11
## GO:0019207 11
## GO:0019887 10
## ID Description GeneRatio
## GO:0071214 GO:0071214 cellular response to abiotic stimulus 22/73
## GO:0104004 GO:0104004 cellular response to environmental stimulus 22/73
## GO:0051402 GO:0051402 neuron apoptotic process 20/73
## GO:0009314 GO:0009314 response to radiation 22/73
## GO:0000082 GO:0000082 G1/S transition of mitotic cell cycle 18/73
## GO:0062197 GO:0062197 cellular response to chemical stress 19/73
## BgRatio pvalue p.adjust qvalue
## GO:0071214 334/18888 1.585558e-21 2.679593e-18 1.126581e-18
## GO:0104004 334/18888 1.585558e-21 2.679593e-18 1.126581e-18
## GO:0051402 292/18888 6.518067e-20 7.343689e-17 3.087505e-17
## GO:0009314 431/18888 3.941464e-19 3.330537e-16 1.400257e-16
## GO:0000082 234/18888 7.352870e-19 4.970540e-16 2.089763e-16
## GO:0062197 311/18888 5.365791e-18 2.702208e-15 1.136089e-15
## geneID
## GO:0071214 MTOR/MAPK8/CDKN1A/ATM/CASP8/PTEN/PARP1/IGF1R/PIK3R1/CHEK1/EGFR/PTGS2/AKT2/CASP9/MYC/CASP3/YAP1/BCL2L1/ITGA2/PIK3CA/MAPK3/TP53BP1
## GO:0104004 MTOR/MAPK8/CDKN1A/ATM/CASP8/PTEN/PARP1/IGF1R/PIK3R1/CHEK1/EGFR/PTGS2/AKT2/CASP9/MYC/CASP3/YAP1/BCL2L1/ITGA2/PIK3CA/MAPK3/TP53BP1
## GO:0051402 RB1/XIAP/BID/FOXO3/ATM/CASP8/KRAS/PARP1/CCND1/AKT2/BCL2/CASP9/AXL/MSH2/CASP3/BCL2L11/BCL2L1/GAPDH/PIK3CA/BRAF
## GO:0009314 AKT1/MAPK8/CDKN1A/ATM/KRAS/PARP1/CCND1/PIK3R1/KIT/EGFR/AKT2/PRKAA1/BCL2/CASP9/MYC/MSH2/CASP3/YAP1/BCL2L1/MSH6/TP53BP1/BRAF
## GO:0000082 RB1/AKT1/ARID1A/BID/CDKN1A/ATM/PTEN/CCNE2/CCND1/EGFR/EZH2/BCL2/E2F1/CDKN2A/MYC/CCNE1/EIF4E/EIF4G1
## GO:0062197 HSPA1A/AKT1/MTOR/MAPK8/FOXO3/ATM/PARP1/EGFR/EZH2/PTGS2/MET/PRKAA1/PXN/AXL/CASP3/MAPK9/PIK3CA/MAPK1/MAPK3
## Count
## GO:0071214 22
## GO:0104004 22
## GO:0051402 20
## GO:0009314 22
## GO:0000082 18
## GO:0062197 19
## ID
## GO:0031968 GO:0031968
## GO:0019867 GO:0019867
## GO:0005741 GO:0005741
## GO:0031143 GO:0031143
## GO:1902911 GO:1902911
## GO:0061695 GO:0061695
## Description
## GO:0031968 organelle outer membrane
## GO:0019867 outer membrane
## GO:0005741 mitochondrial outer membrane
## GO:0031143 pseudopodium
## GO:1902911 protein kinase complex
## GO:0061695 transferase complex, transferring phosphorus-containing groups
## GeneRatio BgRatio pvalue p.adjust qvalue
## GO:0031968 10/73 248/19894 2.359797e-08 3.220903e-06 1.876124e-06
## GO:0019867 10/73 250/19894 2.546168e-08 3.220903e-06 1.876124e-06
## GO:0005741 9/73 219/19894 1.061952e-07 8.955799e-06 5.216609e-06
## GO:0031143 4/73 18/19894 4.910057e-07 3.105611e-05 1.808968e-05
## GO:1902911 7/73 150/19894 1.293568e-06 6.545455e-05 3.812622e-05
## GO:0061695 9/73 308/19894 1.851965e-06 6.908763e-05 4.024243e-05
## geneID Count
## GO:0031968 MTOR/BID/FOXO3/CASP8/KRAS/PTGS2/BCL2/BCL2L11/RAF1/BCL2L1 10
## GO:0019867 MTOR/BID/FOXO3/CASP8/KRAS/PTGS2/BCL2/BCL2L11/RAF1/BCL2L1 10
## GO:0005741 MTOR/BID/FOXO3/CASP8/KRAS/BCL2/BCL2L11/RAF1/BCL2L1 9
## GO:0031143 RAB25/RAF1/MAPK1/MAPK3 4
## GO:1902911 RB1/CDKN1A/IGF1R/CCNE2/CCND1/PRKAA1/CCNE1 7
## GO:0061695 RB1/CDKN1A/IGF1R/CCNE2/CCND1/PIK3R1/PRKAA1/CCNE1/PIK3CA 9
## ID Description GeneRatio
## GO:0140297 GO:0140297 DNA-binding transcription factor binding 9/36
## GO:0019902 GO:0019902 phosphatase binding 6/36
## GO:0019903 GO:0019903 protein phosphatase binding 5/36
## GO:0051219 GO:0051219 phosphoprotein binding 4/36
## GO:0051434 GO:0051434 BH3 domain binding 2/36
## GO:0106310 GO:0106310 protein serine kinase activity 6/36
## BgRatio pvalue p.adjust qvalue
## GO:0140297 478/18522 2.385785e-07 5.415732e-05 2.536466e-05
## GO:0019902 189/18522 1.574359e-06 1.786897e-04 8.368960e-05
## GO:0019903 142/18522 7.683515e-06 5.813860e-04 2.722930e-04
## GO:0051219 93/18522 3.102105e-05 1.760444e-03 8.245067e-04
## GO:0051434 6/18522 5.482548e-05 1.933580e-03 9.055952e-04
## GO:0106310 363/18522 6.442431e-05 1.933580e-03 9.055952e-04
## geneID Count
## GO:0140297 ESR1/BCL2/MYC/RB1/ETS1/ARID1A/YWHAZ/STAT5A/NCOA3 9
## GO:0019902 MET/BCL2/MAPK8/PTK2/MAPK1/PXN 6
## GO:0019903 MET/BCL2/MAPK8/PTK2/PXN 5
## GO:0051219 RB1/YWHAZ/MAPK1/YWHAB 4
## GO:0051434 BCL2/BCL2L1 2
## GO:0106310 AKT2/AKT1/MAPK8/ATM/MAPK1/CHEK1 6
## ID Description
## GO:0051402 GO:0051402 neuron apoptotic process
## GO:0000082 GO:0000082 G1/S transition of mitotic cell cycle
## GO:0044843 GO:0044843 cell cycle G1/S phase transition
## GO:2000045 GO:2000045 regulation of G1/S transition of mitotic cell cycle
## GO:1902806 GO:1902806 regulation of cell cycle G1/S phase transition
## GO:0071214 GO:0071214 cellular response to abiotic stimulus
## GeneRatio BgRatio pvalue p.adjust qvalue
## GO:0051402 11/36 292/18888 4.258731e-12 9.624732e-09 3.868721e-09
## GO:0000082 10/36 234/18888 1.347155e-11 1.522285e-08 6.118921e-09
## GO:0044843 10/36 262/18888 4.112067e-11 2.890359e-08 1.161798e-08
## GO:2000045 9/36 185/18888 5.115680e-11 2.890359e-08 1.161798e-08
## GO:1902806 9/36 211/18888 1.655707e-10 7.483798e-08 3.008159e-08
## GO:0071214 10/36 334/18888 4.419187e-10 1.262827e-07 5.076011e-08
## geneID Count
## GO:0051402 AKT2/G6PD/BCL2/KRAS/CCND1/BCL2L1/RB1/XIAP/BID/ATM/FOXO3 11
## GO:0000082 BCL2/CCND1/AKT1/MYC/RB1/ARID1A/BID/PTEN/ATM/CDKN1A 10
## GO:0044843 BCL2/CCND1/AKT1/MYC/RB1/ARID1A/BID/PTEN/ATM/CDKN1A 10
## GO:2000045 BCL2/CCND1/AKT1/RB1/ARID1A/BID/PTEN/ATM/CDKN1A 9
## GO:1902806 BCL2/CCND1/AKT1/RB1/ARID1A/BID/PTEN/ATM/CDKN1A 9
## GO:0071214 AKT2/IGF1R/MYC/BCL2L1/MAPK8/PTEN/ATM/ITGA2/CDKN1A/CHEK1 10
## ID Description
## GO:0005925 GO:0005925 focal adhesion
## GO:0030055 GO:0030055 cell-substrate junction
## GO:0005741 GO:0005741 mitochondrial outer membrane
## GO:0031968 GO:0031968 organelle outer membrane
## GO:0019867 GO:0019867 outer membrane
## GO:0000307 GO:0000307 cyclin-dependent protein kinase holoenzyme complex
## GeneRatio BgRatio pvalue p.adjust qvalue
## GO:0005925 7/36 421/19894 8.881502e-06 0.0007552391 0.0003974943
## GO:0030055 7/36 431/19894 1.034574e-05 0.0007552391 0.0003974943
## GO:0005741 5/36 219/19894 4.408946e-05 0.0021456872 0.0011293090
## GO:0031968 5/36 248/19894 7.949443e-05 0.0024108652 0.0012688764
## GO:0019867 5/36 250/19894 8.256388e-05 0.0024108652 0.0012688764
## GO:0000307 3/36 56/19894 1.412264e-04 0.0027664851 0.0014560448
## geneID Count
## GO:0005925 KRAS/PTK2/YWHAZ/ITGA2/MAPK1/PXN/YWHAB 7
## GO:0030055 KRAS/PTK2/YWHAZ/ITGA2/MAPK1/PXN/YWHAB 7
## GO:0005741 BCL2/KRAS/BCL2L1/BID/FOXO3 5
## GO:0031968 BCL2/KRAS/BCL2L1/BID/FOXO3 5
## GO:0019867 BCL2/KRAS/BCL2L1/BID/FOXO3 5
## GO:0000307 CCND1/RB1/CDKN1A 3
## NULL
## ID
## GO:1902043 GO:1902043
## GO:0046325 GO:0046325
## GO:0010829 GO:0010829
## GO:1902042 GO:1902042
## GO:1902041 GO:1902041
## GO:2001238 GO:2001238
## Description
## GO:1902043 positive regulation of extrinsic apoptotic signaling pathway via death domain receptors
## GO:0046325 negative regulation of glucose import
## GO:0010829 negative regulation of glucose transmembrane transport
## GO:1902042 negative regulation of extrinsic apoptotic signaling pathway via death domain receptors
## GO:1902041 regulation of extrinsic apoptotic signaling pathway via death domain receptors
## GO:2001238 positive regulation of extrinsic apoptotic signaling pathway
## GeneRatio BgRatio pvalue p.adjust qvalue geneID Count
## GO:1902043 1/1 12/18888 0.0006353240 0.008894536 NA PEA15 1
## GO:0046325 1/1 16/18888 0.0008470987 0.008894536 NA PEA15 1
## GO:0010829 1/1 21/18888 0.0011118170 0.008894536 NA PEA15 1
## GO:1902042 1/1 31/18888 0.0016412537 0.009847522 NA PEA15 1
## GO:1902041 1/1 48/18888 0.0025412961 0.010633318 NA PEA15 1
## GO:2001238 1/1 51/18888 0.0027001271 0.010633318 NA PEA15 1
## ID Description GeneRatio BgRatio
## GO:0005875 GO:0005875 microtubule associated complex 1/1 157/19894
## pvalue p.adjust qvalue geneID Count
## GO:0005875 0.007891827 0.007891827 NA PEA15 1
## ID Description
## GO:0140805 GO:0140805 NAD+-protein-serine ADP-ribosyltransferase activity
## GO:0140294 GO:0140294 NAD DNA ADP-ribosyltransferase activity
## GO:0140807 GO:0140807 NAD+-protein-glutamate ADP-ribosyltransferase activity
## GO:0140806 GO:0140806 NAD+- protein-aspartate ADP-ribosyltransferase activity
## GO:0140537 GO:0140537 transcription regulator activator activity
## GO:0003950 GO:0003950 NAD+ ADP-ribosyltransferase activity
## GeneRatio BgRatio pvalue p.adjust qvalue geneID Count
## GO:0140805 1/1 2/18522 0.0001079797 0.001484721 NA PARP1 1
## GO:0140294 1/1 3/18522 0.0001619695 0.001484721 NA PARP1 1
## GO:0140807 1/1 4/18522 0.0002159594 0.001484721 NA PARP1 1
## GO:0140806 1/1 5/18522 0.0002699492 0.001484721 NA PARP1 1
## GO:0140537 1/1 8/18522 0.0004319188 0.001900443 NA PARP1 1
## GO:0003950 1/1 23/18522 0.0012417665 0.003711802 NA PARP1 1
## ID Description
## GO:1903518 GO:1903518 positive regulation of single strand break repair
## GO:1904762 GO:1904762 positive regulation of myofibroblast differentiation
## GO:0030592 GO:0030592 DNA ADP-ribosylation
## GO:1903516 GO:1903516 regulation of single strand break repair
## GO:1905051 GO:1905051 regulation of base-excision repair
## GO:0071932 GO:0071932 replication fork reversal
## GeneRatio BgRatio pvalue p.adjust qvalue geneID Count
## GO:1903518 1/1 2/18888 0.0001058873 0.005272307 NA PARP1 1
## GO:1904762 1/1 2/18888 0.0001058873 0.005272307 NA PARP1 1
## GO:0030592 1/1 3/18888 0.0001588310 0.005272307 NA PARP1 1
## GO:1903516 1/1 3/18888 0.0001588310 0.005272307 NA PARP1 1
## GO:1905051 1/1 3/18888 0.0001588310 0.005272307 NA PARP1 1
## GO:0071932 1/1 4/18888 0.0002117747 0.005272307 NA PARP1 1
## ID Description GeneRatio BgRatio
## GO:0043596 GO:0043596 nuclear replication fork 1/1 41/19894
## GO:0005657 GO:0005657 replication fork 1/1 74/19894
## GO:0035861 GO:0035861 site of double-strand break 1/1 91/19894
## GO:0090734 GO:0090734 site of DNA damage 1/1 123/19894
## GO:0000781 GO:0000781 chromosome, telomeric region 1/1 173/19894
## GO:0000228 GO:0000228 nuclear chromosome 1/1 226/19894
## pvalue p.adjust qvalue geneID Count
## GO:0043596 0.002060923 0.01219798 NA PARP1 1
## GO:0005657 0.003719714 0.01219798 NA PARP1 1
## GO:0035861 0.004574243 0.01219798 NA PARP1 1
## GO:0090734 0.006182769 0.01236554 NA PARP1 1
## GO:0000781 0.008696089 0.01391374 NA PARP1 1
## GO:0000228 0.011360209 0.01514695 NA PARP1 1
## ID Description GeneRatio
## GO:0045296 GO:0045296 cadherin binding 9/57
## GO:0032143 GO:0032143 single thymine insertion binding 2/57
## GO:0140297 GO:0140297 DNA-binding transcription factor binding 9/57
## GO:0032137 GO:0032137 guanine/thymine mispair binding 2/57
## GO:0032142 GO:0032142 single guanine insertion binding 2/57
## GO:0035173 GO:0035173 histone kinase activity 3/57
## BgRatio pvalue p.adjust qvalue
## GO:0045296 333/18522 7.418914e-07 0.0002737579 0.0001475973
## GO:0032143 2/18522 9.304876e-06 0.0017167495 0.0009255903
## GO:0140297 478/18522 1.409834e-05 0.0017340964 0.0009349428
## GO:0032137 3/18522 2.785936e-05 0.0020560208 0.0011085093
## GO:0032142 3/18522 2.785936e-05 0.0020560208 0.0011085093
## GO:0035173 23/18522 4.684392e-05 0.0025649388 0.0013828938
## geneID Count
## GO:0045296 CTNNA1/EEF2/NDRG1/CDH2/FASN/ANLN/YWHAB/ANXA1/PRDX1 9
## GO:0032143 MSH6/MSH2 2
## GO:0140297 RB1/BCL2/PARP1/GATA3/TP53BP1/ETS1/STAT5A/VHL/AR 9
## GO:0032137 MSH6/MSH2 2
## GO:0032142 MSH6/MSH2 2
## GO:0035173 PRKCA/CDK1/ATM 3
## ID Description GeneRatio BgRatio
## GO:0051402 GO:0051402 neuron apoptotic process 13/57 292/18888
## GO:0030879 GO:0030879 mammary gland development 10/57 135/18888
## GO:0051146 GO:0051146 striated muscle cell differentiation 12/57 313/18888
## GO:0048872 GO:0048872 homeostasis of number of cells 12/57 322/18888
## GO:0002520 GO:0002520 immune system development 10/57 197/18888
## GO:0048732 GO:0048732 gland development 13/57 449/18888
## pvalue p.adjust qvalue
## GO:0051402 2.941388e-12 8.621207e-09 3.966229e-09
## GO:0030879 8.059497e-12 1.181119e-08 5.433798e-09
## GO:0051146 1.262295e-10 1.233262e-07 5.673683e-08
## GO:0048872 1.749112e-10 1.281662e-07 5.896350e-08
## GO:0002520 3.418142e-10 2.003715e-07 9.218189e-08
## GO:0048732 6.159712e-10 3.009019e-07 1.384314e-07
## geneID
## GO:0051402 RB1/XIAP/BCL2/BCL2L11/PARP1/GATA3/AKT1S1/GSK3A/COL6A1/G6PD/ATM/GAPDH/MSH2
## GO:0030879 AKT1/BCL2L11/GATA3/NRG1/MAPK1/FASN/STAT5A/BRCA2/AR/XBP1
## GO:0051146 RB1/AKT1/BCL2/NRG1/GSK3A/CDH2/CDK1/COL6A1/G6PD/TSC1/XBP1/MYH11
## GO:0048872 RB1/XIAP/AKT1/BCL2/BCL2L11/GATA3/CDH2/ETS1/COL6A1/ANXA1/G6PD/PRDX1
## GO:0002520 BCL2/BCL2L11/GATA3/MAPK1/TFRC/TP53BP1/MSH6/RBM15/ATM/MSH2
## GO:0048732 AKT1/BCL2/BCL2L11/GATA3/NRG1/MAPK1/FASN/TYMS/STAT5A/ATM/BRCA2/AR/XBP1
## Count
## GO:0051402 13
## GO:0030879 10
## GO:0051146 12
## GO:0048872 12
## GO:0002520 10
## GO:0048732 13
## ID Description GeneRatio BgRatio
## GO:0032301 GO:0032301 MutSalpha complex 2/57 2/19894
## GO:0097125 GO:0097125 cyclin B1-CDK1 complex 2/57 2/19894
## GO:0000781 GO:0000781 chromosome, telomeric region 6/57 173/19894
## GO:0042470 GO:0042470 melanosome 5/57 112/19894
## GO:0048770 GO:0048770 pigment granule 5/57 112/19894
## GO:1990391 GO:1990391 DNA repair complex 3/57 22/19894
## pvalue p.adjust qvalue
## GO:0032301 8.065671e-06 0.0007273642 0.0004265245
## GO:0097125 8.065671e-06 0.0007273642 0.0004265245
## GO:0000781 9.963893e-06 0.0007273642 0.0004265245
## GO:0042470 1.714196e-05 0.0007508176 0.0004402776
## GO:0048770 1.714196e-05 0.0007508176 0.0004402776
## GO:1990391 3.304014e-05 0.0012059651 0.0007071749
## geneID Count
## GO:0032301 MSH6/MSH2 2
## GO:0097125 CDK1/CCNB1 2
## GO:0000781 PARP1/TP53BP1/CDK1/ATM/BRCA2/MSH2 6
## GO:0042470 TFRC/FASN/YWHAB/PRDX1/MYH11 5
## GO:0048770 TFRC/FASN/YWHAB/PRDX1/MYH11 5
## GO:1990391 TP53BP1/ATM/BRCA2 3
## ID
## GO:0140297 GO:0140297
## GO:0019902 GO:0019902
## GO:0004674 GO:0004674
## GO:0106310 GO:0106310
## GO:0019903 GO:0019903
## GO:0016538 GO:0016538
## Description
## GO:0140297 DNA-binding transcription factor binding
## GO:0019902 phosphatase binding
## GO:0004674 protein serine/threonine kinase activity
## GO:0106310 protein serine kinase activity
## GO:0019903 protein phosphatase binding
## GO:0016538 cyclin-dependent protein serine/threonine kinase regulator activity
## GeneRatio BgRatio pvalue p.adjust qvalue
## GO:0140297 19/83 478/18522 2.598024e-13 1.158719e-10 5.360134e-11
## GO:0019902 13/83 189/18522 2.434097e-12 5.428037e-10 2.510964e-10
## GO:0004674 15/83 427/18522 6.289373e-10 6.862943e-08 3.174739e-08
## GO:0106310 14/83 363/18522 7.479241e-10 6.862943e-08 3.174739e-08
## GO:0019903 10/83 142/18522 7.693883e-10 6.862943e-08 3.174739e-08
## GO:0016538 7/83 50/18522 2.397033e-09 1.775943e-07 8.215361e-08
## geneID
## GO:0140297 ESR1/BCL2/RB1/VHL/ETS1/ARID1A/PARP1/AR/EIF4E/STAT5A/NCOA3/E2F1/CDKN2A/MYC/YAP1/SMAD3/SMAD4/MAPK3/TP53BP1
## GO:0019902 MET/BCL2/MAPK8/PTK2/MAPT/PIK3R1/CDKN1B/EGFR/PXN/SMAD3/MAPK1/MAPK3/YWHAE
## GO:0004674 AKT1/MTOR/MAPK8/ATM/CHEK1/EGFR/AKT2/PRKAA1/MAPK9/RAF1/PIK3CA/PRKCA/MAPK1/MAPK3/BRAF
## GO:0106310 AKT1/MTOR/MAPK8/ATM/CHEK1/AKT2/PRKAA1/MAPK9/RAF1/PIK3CA/PRKCA/MAPK1/MAPK3/BRAF
## GO:0019903 MET/BCL2/MAPK8/PTK2/MAPT/PIK3R1/CDKN1B/EGFR/PXN/YWHAE
## GO:0016538 CCND1/CDKN1A/CCNE2/CDKN1B/CDKN2A/CASP3/CCNE1
## Count
## GO:0140297 19
## GO:0019902 13
## GO:0004674 15
## GO:0106310 14
## GO:0019903 10
## GO:0016538 7
## ID Description GeneRatio
## GO:0071214 GO:0071214 cellular response to abiotic stimulus 24/83
## GO:0104004 GO:0104004 cellular response to environmental stimulus 24/83
## GO:0009314 GO:0009314 response to radiation 24/83
## GO:0051402 GO:0051402 neuron apoptotic process 21/83
## GO:0062197 GO:0062197 cellular response to chemical stress 21/83
## GO:0000082 GO:0000082 G1/S transition of mitotic cell cycle 19/83
## BgRatio pvalue p.adjust qvalue
## GO:0071214 334/18888 6.820553e-23 1.250207e-19 5.251826e-20
## GO:0104004 334/18888 6.820553e-23 1.250207e-19 5.251826e-20
## GO:0009314 431/18888 2.798088e-20 3.419264e-17 1.436352e-17
## GO:0051402 292/18888 4.741770e-20 4.345832e-17 1.825581e-17
## GO:0062197 311/18888 1.756370e-19 1.287770e-16 5.409619e-17
## GO:0000082 234/18888 3.550507e-19 2.169360e-16 9.112969e-17
## geneID
## GO:0071214 IGF1R/CDKN1A/MTOR/MAPK8/ATM/CASP8/PTEN/PARP1/RAD51/ERCC1/PIK3R1/CHEK1/EGFR/PTGS2/AKT2/CASP9/MYC/CASP3/YAP1/BCL2L1/ITGA2/PIK3CA/MAPK3/TP53BP1
## GO:0104004 IGF1R/CDKN1A/MTOR/MAPK8/ATM/CASP8/PTEN/PARP1/RAD51/ERCC1/PIK3R1/CHEK1/EGFR/PTGS2/AKT2/CASP9/MYC/CASP3/YAP1/BCL2L1/ITGA2/PIK3CA/MAPK3/TP53BP1
## GO:0009314 BCL2/KRAS/CCND1/AKT1/CDKN1A/MAPK8/ATM/PARP1/RAD51/ERCC1/PIK3R1/KIT/EGFR/AKT2/PRKAA1/CASP9/MYC/MSH2/CASP3/YAP1/BCL2L1/MSH6/TP53BP1/BRAF
## GO:0051402 G6PD/BCL2/KRAS/CCND1/RB1/XIAP/BID/FOXO3/ATM/CASP8/PARP1/BCL2L11/AKT2/CASP9/AXL/MSH2/CASP3/BCL2L1/GAPDH/PIK3CA/BRAF
## GO:0062197 MET/G6PD/AKT1/HSPA1A/MTOR/MAPK8/FOXO3/ATM/PARP1/MAPT/EGFR/EZH2/PTGS2/PRKAA1/PXN/AXL/CASP3/MAPK9/PIK3CA/MAPK1/MAPK3
## GO:0000082 BCL2/CCND1/AKT1/RB1/CDKN1A/ARID1A/BID/ATM/PTEN/CCNE2/EIF4E/CDKN1B/EGFR/EZH2/E2F1/CDKN2A/MYC/CCNE1/EIF4G1
## Count
## GO:0071214 24
## GO:0104004 24
## GO:0009314 24
## GO:0051402 21
## GO:0062197 21
## GO:0000082 19
## ID Description GeneRatio BgRatio
## GO:0031968 GO:0031968 organelle outer membrane 10/83 248/19894
## GO:0019867 GO:0019867 outer membrane 10/83 250/19894
## GO:0005741 GO:0005741 mitochondrial outer membrane 9/83 219/19894
## GO:0000781 GO:0000781 chromosome, telomeric region 8/83 173/19894
## GO:0031143 GO:0031143 pseudopodium 4/83 18/19894
## GO:1902911 GO:1902911 protein kinase complex 7/83 150/19894
## pvalue p.adjust qvalue
## GO:0031968 8.283767e-08 1.285895e-05 7.613853e-06
## GO:0019867 8.929827e-08 1.285895e-05 7.613853e-06
## GO:0005741 3.269219e-07 3.138451e-05 1.858293e-05
## GO:0000781 6.297686e-07 4.534334e-05 2.684803e-05
## GO:0031143 8.243131e-07 4.748044e-05 2.811342e-05
## GO:1902911 3.095495e-06 1.485838e-04 8.797724e-05
## geneID Count
## GO:0031968 BCL2/KRAS/MTOR/BID/FOXO3/CASP8/BCL2L11/PTGS2/RAF1/BCL2L1 10
## GO:0019867 BCL2/KRAS/MTOR/BID/FOXO3/CASP8/BCL2L11/PTGS2/RAF1/BCL2L1 10
## GO:0005741 BCL2/KRAS/MTOR/BID/FOXO3/CASP8/BCL2L11/RAF1/BCL2L1 9
## GO:0000781 ATM/PARP1/RAD51/ERCC1/CHEK1/EZH2/MSH2/TP53BP1 8
## GO:0031143 RAB25/RAF1/MAPK1/MAPK3 4
## GO:1902911 CCND1/IGF1R/RB1/CDKN1A/CCNE2/PRKAA1/CCNE1 7
## ID
## GO:0106017 GO:0106017
## GO:0030544 GO:0030544
## GO:0001618 GO:0001618
## GO:0140272 GO:0140272
## GO:0052745 GO:0052745
## GO:0035173 GO:0035173
## Description GeneRatio
## GO:0106017 phosphatidylinositol-3,4-bisphosphate phosphatase activity 2/19
## GO:0030544 Hsp70 protein binding 3/19
## GO:0001618 virus receptor activity 3/19
## GO:0140272 exogenous protein binding 3/19
## GO:0052745 inositol phosphate phosphatase activity 2/19
## GO:0035173 histone kinase activity 2/19
## BgRatio pvalue p.adjust qvalue geneID Count
## GO:0106017 4/18522 5.974387e-06 0.0008722605 0.0004213515 PTEN/INPP4B 2
## GO:0030544 51/18522 1.847373e-05 0.0013485820 0.0006514419 TSC1/CDK1/TFRC 3
## GO:0001618 79/18522 6.888881e-05 0.0026107139 0.0012611235 EGFR/CDK1/TFRC 3
## GO:0140272 80/18522 7.152641e-05 0.0026107139 0.0012611235 EGFR/CDK1/TFRC 3
## GO:0052745 18/18522 1.510472e-04 0.0044105795 0.0021305611 PTEN/INPP4B 2
## GO:0035173 23/18522 2.490081e-04 0.0049183110 0.0023758244 ATM/CDK1 2
## ID Description
## GO:0045785 GO:0045785 positive regulation of cell adhesion
## GO:0031667 GO:0031667 response to nutrient levels
## GO:0007584 GO:0007584 response to nutrient
## GO:0035051 GO:0035051 cardiocyte differentiation
## GO:0002520 GO:0002520 immune system development
## GO:0002285 GO:0002285 lymphocyte activation involved in immune response
## GeneRatio BgRatio pvalue p.adjust qvalue
## GO:0045785 7/19 485/18888 2.718156e-07 0.0002112691 9.142344e-05
## GO:0031667 7/19 490/18888 2.913520e-07 0.0002112691 9.142344e-05
## GO:0007584 5/19 164/18888 4.892463e-07 0.0002112691 9.142344e-05
## GO:0035051 5/19 165/18888 5.042222e-07 0.0002112691 9.142344e-05
## GO:0002520 5/19 197/18888 1.211298e-06 0.0004060271 1.757020e-04
## GO:0002285 5/19 212/18888 1.738338e-06 0.0004340875 1.878447e-04
## geneID Count
## GO:0045785 IGFBP2/GATA3/ATM/TSC1/XBP1/TFRC/PREX1 7
## GO:0031667 G6PD/IGFBP2/EGFR/TSC1/XBP1/ERCC1/TFRC 7
## GO:0007584 IGFBP2/EGFR/XBP1/ERCC1/TFRC 5
## GO:0035051 G6PD/EGFR/TSC1/PDCD4/CDK1 5
## GO:0002520 RBM15/GATA3/ATM/ERCC1/TFRC 5
## GO:0002285 GATA3/TSC1/XBP1/ERCC1/TFRC 5
## ID Description GeneRatio
## GO:0000781 GO:0000781 chromosome, telomeric region 3/19
## GO:0070435 GO:0070435 Shc-EGFR complex 1/19
## GO:0097122 GO:0097122 cyclin A2-CDK1 complex 1/19
## GO:0097125 GO:0097125 cyclin B1-CDK1 complex 1/19
## GO:0030669 GO:0030669 clathrin-coated endocytic vesicle membrane 2/19
## GO:0000110 GO:0000110 nucleotide-excision repair factor 1 complex 1/19
## BgRatio pvalue p.adjust qvalue geneID Count
## GO:0000781 173/19894 0.0005652514 0.03700613 0.02048088 ATM/CDK1/ERCC1 3
## GO:0070435 2/19894 0.0019092595 0.03700613 0.02048088 EGFR 1
## GO:0097122 2/19894 0.0019092595 0.03700613 0.02048088 CDK1 1
## GO:0097125 2/19894 0.0019092595 0.03700613 0.02048088 CDK1 1
## GO:0030669 75/19894 0.0023004924 0.03700613 0.02048088 EGFR/TFRC 2
## GO:0000110 3/19894 0.0028625937 0.03700613 0.02048088 ERCC1 1
## ID Description GeneRatio
## GO:0019902 GO:0019902 phosphatase binding 11/55
## GO:0140297 GO:0140297 DNA-binding transcription factor binding 14/55
## GO:0106310 GO:0106310 protein serine kinase activity 11/55
## GO:0004674 GO:0004674 protein serine/threonine kinase activity 11/55
## GO:0004707 GO:0004707 MAP kinase activity 4/55
## GO:0019903 GO:0019903 protein phosphatase binding 7/55
## BgRatio pvalue p.adjust qvalue
## GO:0019902 189/18522 7.547525e-12 2.211425e-09 1.056653e-09
## GO:0140297 478/18522 7.957760e-11 1.165812e-08 5.570432e-09
## GO:0106310 363/18522 7.793334e-09 7.611489e-07 3.636889e-07
## GO:0004674 427/18522 4.131281e-08 3.026163e-06 1.445948e-06
## GO:0004707 16/18522 1.233117e-07 7.226064e-06 3.452727e-06
## GO:0019903 142/18522 2.002443e-07 9.778597e-06 4.672367e-06
## geneID
## GO:0019902 MET/BCL2/MAPK8/PTK2/MAPK1/PXN/PIK3R1/CTNNB1/SMAD3/MAPK3/TSC2
## GO:0140297 ESR1/BCL2/MYC/RB1/ETS1/ARID1A/YWHAZ/STAT5A/NCOA3/E2F1/CDKN2A/CTNNB1/SMAD3/MAPK3
## GO:0106310 AKT2/AKT1/MAPK8/ATM/MAPK1/CHEK1/RAF1/PRKAA1/MAPK9/PRKCA/MAPK3
## GO:0004674 AKT2/AKT1/MAPK8/ATM/MAPK1/CHEK1/RAF1/PRKAA1/MAPK9/PRKCA/MAPK3
## GO:0004707 MAPK8/MAPK1/MAPK9/MAPK3
## GO:0019903 MET/BCL2/MAPK8/PTK2/PXN/PIK3R1/CTNNB1
## Count
## GO:0019902 11
## GO:0140297 14
## GO:0106310 11
## GO:0004674 11
## GO:0004707 4
## GO:0019903 7
## ID Description
## GO:0051402 GO:0051402 neuron apoptotic process
## GO:0000082 GO:0000082 G1/S transition of mitotic cell cycle
## GO:1901653 GO:1901653 cellular response to peptide
## GO:2000045 GO:2000045 regulation of G1/S transition of mitotic cell cycle
## GO:0071375 GO:0071375 cellular response to peptide hormone stimulus
## GO:0044843 GO:0044843 cell cycle G1/S phase transition
## GeneRatio BgRatio pvalue p.adjust qvalue
## GO:0051402 14/55 292/18888 8.050039e-14 1.127091e-10 4.913583e-11
## GO:0000082 13/55 234/18888 1.061998e-13 1.127091e-10 4.913583e-11
## GO:1901653 15/55 376/18888 1.336328e-13 1.127091e-10 4.913583e-11
## GO:2000045 12/55 185/18888 1.654398e-13 1.127091e-10 4.913583e-11
## GO:0071375 14/55 311/18888 1.908383e-13 1.127091e-10 4.913583e-11
## GO:0044843 13/55 262/18888 4.517177e-13 1.926300e-10 8.397758e-11
## geneID
## GO:0051402 AKT2/G6PD/BCL2/KRAS/CCND1/BCL2L1/RB1/XIAP/BID/ATM/CASP9/AXL/FOXO3/CTNNB1
## GO:0000082 BCL2/CCND1/AKT1/MYC/RB1/ARID1A/BID/PTEN/ATM/CDKN1A/E2F1/CDKN2A/CCNE1
## GO:1901653 AKT2/AKT1/IGF1R/RB1/PTK2/MAPK1/PXN/PIK3R1/STAT5A/RAF1/PRKAA1/FOXO3/PRKCA/MAPK3/TSC2
## GO:2000045 BCL2/CCND1/AKT1/RB1/ARID1A/BID/PTEN/ATM/CDKN1A/E2F1/CDKN2A/CCNE1
## GO:0071375 AKT2/AKT1/IGF1R/RB1/PTK2/MAPK1/PXN/PIK3R1/STAT5A/RAF1/PRKAA1/PRKCA/MAPK3/TSC2
## GO:0044843 BCL2/CCND1/AKT1/MYC/RB1/ARID1A/BID/PTEN/ATM/CDKN1A/E2F1/CDKN2A/CCNE1
## Count
## GO:0051402 14
## GO:0000082 13
## GO:1901653 15
## GO:2000045 12
## GO:0071375 14
## GO:0044843 13
## ID Description
## GO:0005925 GO:0005925 focal adhesion
## GO:0030055 GO:0030055 cell-substrate junction
## GO:1902911 GO:1902911 protein kinase complex
## GO:0090571 GO:0090571 RNA polymerase II transcription repressor complex
## GO:0031143 GO:0031143 pseudopodium
## GO:0000307 GO:0000307 cyclin-dependent protein kinase holoenzyme complex
## GeneRatio BgRatio pvalue p.adjust qvalue
## GO:0005925 9/55 421/19894 2.099265e-06 0.0002475384 0.0001446208
## GO:0030055 9/55 431/19894 2.544248e-06 0.0002475384 0.0001446208
## GO:1902911 6/55 150/19894 3.553183e-06 0.0002475384 0.0001446208
## GO:0090571 3/55 15/19894 8.886276e-06 0.0004643079 0.0002712653
## GO:0031143 3/55 18/19894 1.584326e-05 0.0006011223 0.0003511971
## GO:0000307 4/55 56/19894 1.725710e-05 0.0006011223 0.0003511971
## geneID Count
## GO:0005925 KRAS/PTK2/YWHAZ/ITGA2/MAPK1/PXN/YWHAB/CTNNB1/MAPK3 9
## GO:0030055 KRAS/PTK2/YWHAZ/ITGA2/MAPK1/PXN/YWHAB/CTNNB1/MAPK3 9
## GO:1902911 CCND1/IGF1R/RB1/CDKN1A/PRKAA1/CCNE1 6
## GO:0090571 MYC/FOXO3/CTNNB1 3
## GO:0031143 MAPK1/RAF1/MAPK3 3
## GO:0000307 CCND1/RB1/CDKN1A/CCNE1 4
## ID
## GO:0004365 GO:0004365
## GO:0043891 GO:0043891
## GO:0019838 GO:0019838
## GO:0005006 GO:0005006
## GO:1990599 GO:1990599
## GO:0048408 GO:0048408
## Description
## GO:0004365 glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity
## GO:0043891 glyceraldehyde-3-phosphate dehydrogenase (NAD(P)+) (phosphorylating) activity
## GO:0019838 growth factor binding
## GO:0005006 epidermal growth factor receptor activity
## GO:1990599 3' overhang single-stranded DNA endodeoxyribonuclease activity
## GO:0048408 epidermal growth factor binding
## GeneRatio BgRatio pvalue p.adjust qvalue geneID
## GO:0004365 1/6 2/18522 0.0006477907 0.01321315 0.003886220 GAPDH
## GO:0043891 1/6 2/18522 0.0006477907 0.01321315 0.003886220 GAPDH
## GO:0019838 2/6 135/18522 0.0007759748 0.01321315 0.003886220 IGFBP2/EGFR
## GO:0005006 1/6 3/18522 0.0009715550 0.01321315 0.003886220 EGFR
## GO:1990599 1/6 3/18522 0.0009715550 0.01321315 0.003886220 ERCC1
## GO:0048408 1/6 4/18522 0.0012952318 0.01467929 0.004317439 EGFR
## Count
## GO:0004365 1
## GO:0043891 1
## GO:0019838 2
## GO:0005006 1
## GO:1990599 1
## GO:0048408 1
## ID Description
## GO:0031667 GO:0031667 response to nutrient levels
## GO:0007584 GO:0007584 response to nutrient
## GO:0048009 GO:0048009 insulin-like growth factor receptor signaling pathway
## GO:0046686 GO:0046686 response to cadmium ion
## GO:0032355 GO:0032355 response to estradiol
## GO:0035606 GO:0035606 peptidyl-cysteine S-trans-nitrosylation
## GeneRatio BgRatio pvalue p.adjust qvalue
## GO:0031667 4/6 490/18888 6.439864e-06 0.004274971 0.001719015
## GO:0007584 3/6 164/18888 1.261053e-05 0.004274971 0.001719015
## GO:0048009 2/6 53/18888 1.150515e-04 0.025023966 0.010062424
## GO:0046686 2/6 60/18888 1.476340e-04 0.025023966 0.010062424
## GO:0032355 2/6 115/18888 5.425086e-04 0.034719489 0.013961105
## GO:0035606 1/6 2/18888 6.352399e-04 0.034719489 0.013961105
## geneID Count
## GO:0031667 IGFBP2/EGFR/TSC1/ERCC1 4
## GO:0007584 IGFBP2/EGFR/ERCC1 3
## GO:0048009 IGFBP2/ERCC1 2
## GO:0046686 EGFR/ERCC1 2
## GO:0032355 IGFBP2/EGFR 2
## GO:0035606 GAPDH 1
## ID Description GeneRatio
## GO:0031965 GO:0031965 nuclear membrane 3/6
## GO:0005635 GO:0005635 nuclear envelope 3/6
## GO:0005811 GO:0005811 lipid droplet 2/6
## GO:0070435 GO:0070435 Shc-EGFR complex 1/6
## GO:0000110 GO:0000110 nucleotide-excision repair factor 1 complex 1/6
## GO:0033596 GO:0033596 TSC1-TSC2 complex 1/6
## BgRatio pvalue p.adjust qvalue geneID
## GO:0031965 313/19894 7.448714e-05 0.004022305 0.002430633 RBM15/EGFR/GAPDH
## GO:0005635 498/19894 2.947677e-04 0.007208863 0.004356233 RBM15/EGFR/GAPDH
## GO:0005811 104/19894 4.004924e-04 0.007208863 0.004356233 TSC1/GAPDH
## GO:0070435 2/19894 6.031211e-04 0.008140089 0.004918962 EGFR
## GO:0000110 3/19894 9.045680e-04 0.008140089 0.004918962 ERCC1
## GO:0033596 4/19894 1.205939e-03 0.008140089 0.004918962 TSC1
## Count
## GO:0031965 3
## GO:0005635 3
## GO:0005811 2
## GO:0070435 1
## GO:0000110 1
## GO:0033596 1
## ID
## GO:0050661 GO:0050661
## GO:0004066 GO:0004066
## GO:0004345 GO:0004345
## GO:0004365 GO:0004365
## GO:0043891 GO:0043891
## GO:0005006 GO:0005006
## Description
## GO:0050661 NADP binding
## GO:0004066 asparagine synthase (glutamine-hydrolyzing) activity
## GO:0004345 glucose-6-phosphate dehydrogenase activity
## GO:0004365 glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity
## GO:0043891 glyceraldehyde-3-phosphate dehydrogenase (NAD(P)+) (phosphorylating) activity
## GO:0005006 epidermal growth factor receptor activity
## GeneRatio BgRatio pvalue p.adjust qvalue geneID
## GO:0050661 2/7 53/18522 0.0001671697 0.01088259 0.005727679 G6PD/GAPDH
## GO:0004066 1/7 2/18522 0.0007557355 0.01088259 0.005727679 ASNS
## GO:0004345 1/7 2/18522 0.0007557355 0.01088259 0.005727679 G6PD
## GO:0004365 1/7 2/18522 0.0007557355 0.01088259 0.005727679 GAPDH
## GO:0043891 1/7 2/18522 0.0007557355 0.01088259 0.005727679 GAPDH
## GO:0005006 1/7 3/18522 0.0011334196 0.01360104 0.007158439 EGFR
## Count
## GO:0050661 2
## GO:0004066 1
## GO:0004345 1
## GO:0004365 1
## GO:0043891 1
## GO:0005006 1
## ID Description GeneRatio
## GO:0072593 GO:0072593 reactive oxygen species metabolic process 3/7
## GO:0051402 GO:0051402 neuron apoptotic process 3/7
## GO:1902895 GO:1902895 positive regulation of miRNA transcription 2/7
## GO:2000630 GO:2000630 positive regulation of miRNA metabolic process 2/7
## GO:0006801 GO:0006801 superoxide metabolic process 2/7
## GO:0003281 GO:0003281 ventricular septum development 2/7
## BgRatio pvalue p.adjust qvalue geneID Count
## GO:0072593 238/18888 6.661039e-05 0.02735276 0.01105678 G6PD/EGFR/PREX1 3
## GO:0051402 292/18888 1.222423e-04 0.02735276 0.01105678 G6PD/GATA3/GAPDH 3
## GO:1902895 56/18888 1.795889e-04 0.02735276 0.01105678 GATA3/EGFR 2
## GO:2000630 67/18888 2.573377e-04 0.02735276 0.01105678 GATA3/EGFR 2
## GO:0006801 73/18888 3.055481e-04 0.02735276 0.01105678 EGFR/PREX1 2
## GO:0003281 74/18888 3.139800e-04 0.02735276 0.01105678 RBM15/GATA3 2
## ID Description
## GO:0031965 GO:0031965 nuclear membrane
## GO:0005635 GO:0005635 nuclear envelope
## GO:0070435 GO:0070435 Shc-EGFR complex
## GO:0097452 GO:0097452 GAIT complex
## GO:0097487 GO:0097487 multivesicular body, internal vesicle
## GO:0036396 GO:0036396 RNA N6-methyladenosine methyltransferase complex
## GeneRatio BgRatio pvalue p.adjust qvalue
## GO:0031965 3/7 313/19894 0.0001288323 0.00566862 0.003797162
## GO:0005635 3/7 498/19894 0.0005062513 0.01031981 0.006912794
## GO:0070435 1/7 2/19894 0.0007036236 0.01031981 0.006912794
## GO:0097452 1/7 4/19894 0.0014068229 0.01547505 0.010366063
## GO:0097487 1/7 6/19894 0.0021095979 0.01856446 0.012435525
## GO:0036396 1/7 9/19894 0.0031629656 0.02319508 0.015537375
## geneID Count
## GO:0031965 RBM15/EGFR/GAPDH 3
## GO:0005635 RBM15/EGFR/GAPDH 3
## GO:0070435 EGFR 1
## GO:0097452 GAPDH 1
## GO:0097487 EGFR 1
## GO:0036396 RBM15 1
## ID
## GO:0005113 GO:0005113
## GO:0008353 GO:0008353
## GO:0061575 GO:0061575
## GO:0035173 GO:0035173
## GO:0140994 GO:0140994
## GO:0004693 GO:0004693
## Description
## GO:0005113 patched binding
## GO:0008353 RNA polymerase II CTD heptapeptide repeat kinase activity
## GO:0061575 cyclin-dependent protein serine/threonine kinase activator activity
## GO:0035173 histone kinase activity
## GO:0140994 RNA polymerase II CTD heptapeptide repeat modifying activity
## GO:0004693 cyclin-dependent protein serine/threonine kinase activity
## GeneRatio BgRatio pvalue p.adjust qvalue geneID Count
## GO:0005113 1/5 8/18522 0.002157962 0.0289896 0.01056301 CCNB1 1
## GO:0008353 1/5 10/18522 0.002696870 0.0289896 0.01056301 CDK1 1
## GO:0061575 1/5 16/18522 0.004312197 0.0289896 0.01056301 CCNB1 1
## GO:0035173 1/5 23/18522 0.006194099 0.0289896 0.01056301 CDK1 1
## GO:0140994 1/5 23/18522 0.006194099 0.0289896 0.01056301 CDK1 1
## GO:0004693 1/5 29/18522 0.007804892 0.0289896 0.01056301 CDK1 1
## ID
## GO:1905448 GO:1905448
## GO:1905446 GO:1905446
## GO:0044772 GO:0044772
## GO:0000086 GO:0000086
## GO:0044839 GO:0044839
## GO:1902850 GO:1902850
## Description
## GO:1905448 positive regulation of mitochondrial ATP synthesis coupled electron transport
## GO:1905446 regulation of mitochondrial ATP synthesis coupled electron transport
## GO:0044772 mitotic cell cycle phase transition
## GO:0000086 G2/M transition of mitotic cell cycle
## GO:0044839 cell cycle G2/M phase transition
## GO:1902850 microtubule cytoskeleton organization involved in mitosis
## GeneRatio BgRatio pvalue p.adjust qvalue
## GO:1905448 2/5 4/18888 3.363104e-07 0.0001069467 2.584280e-05
## GO:1905446 2/5 7/18888 1.176712e-06 0.0001668324 4.031369e-05
## GO:0044772 4/5 451/18888 1.573891e-06 0.0001668324 4.031369e-05
## GO:0000086 3/5 136/18888 3.613177e-06 0.0002872476 6.941103e-05
## GO:0044839 3/5 152/18888 5.049737e-06 0.0003211632 7.760648e-05
## GO:1902850 3/5 164/18888 6.345810e-06 0.0003363279 8.127090e-05
## geneID Count
## GO:1905448 CDK1/CCNB1 2
## GO:1905446 CDK1/CCNB1 2
## GO:0044772 ANLN/CDK1/CCNB1/FOXM1 4
## GO:0000086 CDK1/CCNB1/FOXM1 3
## GO:0044839 CDK1/CCNB1/FOXM1 3
## GO:1902850 STMN1/CDK1/CCNB1 3
## ID Description
## GO:0097125 GO:0097125 cyclin B1-CDK1 complex
## GO:0000307 GO:0000307 cyclin-dependent protein kinase holoenzyme complex
## GO:1902554 GO:1902554 serine/threonine protein kinase complex
## GO:0097122 GO:0097122 cyclin A2-CDK1 complex
## GO:1902911 GO:1902911 protein kinase complex
## GO:0005826 GO:0005826 actomyosin contractile ring
## GeneRatio BgRatio pvalue p.adjust qvalue
## GO:0097125 2/5 2/19894 5.053678e-08 1.364493e-06 1.595898e-07
## GO:0000307 2/5 56/19894 7.740495e-05 1.044967e-03 1.222183e-04
## GO:1902554 2/5 136/19894 4.577086e-04 3.004513e-03 3.514051e-04
## GO:0097122 1/5 2/19894 5.026136e-04 3.004513e-03 3.514051e-04
## GO:1902911 2/5 150/19894 5.563914e-04 3.004513e-03 3.514051e-04
## GO:0005826 1/5 4/19894 1.005025e-03 3.993377e-03 4.670617e-04
## geneID Count
## GO:0097125 CDK1/CCNB1 2
## GO:0000307 CDK1/CCNB1 2
## GO:1902554 CDK1/CCNB1 2
## GO:0097122 CDK1 1
## GO:1902911 CDK1/CCNB1 2
## GO:0005826 ANLN 1barplot(ego_MF[[1]], title = "enrichGO, Molecular Function, Factor 1 of 1")
barplot(ego_MF[[2]], title = "enrichGO, Molecular Function, Factor 1 of 2")
barplot(ego_MF[[3]], title = "enrichGO, Molecular Function, Factor 2 of 2")
barplot(ego_MF[[4]], title = "enrichGO, Molecular Function, Factor 1 of 3")
barplot(ego_MF[[5]], title = "enrichGO, Molecular Function, Factor 2 of 3")
#barplot(ego_MF[[6]], title = "enrichGO, Molecular Function, Factor 3 of 3")
barplot(ego_MF[[7]], title = "enrichGO, Molecular Function, Factor 1 of 5")
barplot(ego_MF[[8]], title = "enrichGO, Molecular Function, Factor 2 of 5")
barplot(ego_MF[[9]], title = "enrichGO, Molecular Function, Factor 3 of 5")
#barplot(ego_MF[[10]], title = "enrichGO, Molecular Function, Factor 4 of 5")
barplot(ego_MF[[11]], title = "enrichGO, Molecular Function, Factor 5 of 5")
barplot(ego_MF[[12]], title = "enrichGO, Molecular Function, Factor 1 of 10")
barplot(ego_MF[[13]], title = "enrichGO, Molecular Function, Factor 2 of 10")
barplot(ego_MF[[14]], title = "enrichGO, Molecular Function, Factor 3 of 10")
barplot(ego_MF[[15]], title = "enrichGO, Molecular Function, Factor 4 of 10")
barplot(ego_MF[[16]], title = "enrichGO, Molecular Function, Factor 5 of 10")
barplot(ego_MF[[17]], title = "enrichGO, Molecular Function, Factor 6 of 10")
barplot(ego_MF[[18]], title = "enrichGO, Molecular Function, Factor 7 of 10")
#barplot(ego_MF[[19]], title = "enrichGO, Molecular Function, Factor 8 of 10")
#barplot(ego_MF[[20]], title = "enrichGO, Molecular Function, Factor 9 of 10")
#barplot(ego_MF[[21]], title = "enrichGO, Molecular Function, Factor 10 of 10")
barplot(ego_BP[[1]], title = "enrichGO, Biological Process, Factor 1 of 1")
barplot(ego_BP[[2]], title = "enrichGO, Biological Process, Factor 1 of 2")
barplot(ego_BP[[3]], title = "enrichGO, Biological Process, Factor 2 of 2")
barplot(ego_BP[[4]], title = "enrichGO, Biological Process, Factor 1 of 3")
barplot(ego_BP[[5]], title = "enrichGO, Biological Process, Factor 2 of 3")
#barplot(ego_BP[[6]], title = "enrichGO, Biological Process, Factor 3 of 3")
barplot(ego_BP[[7]], title = "enrichGO, Biological Process, Factor 1 of 5")
barplot(ego_BP[[8]], title = "enrichGO, Biological Process, Factor 2 of 5")
barplot(ego_BP[[9]], title = "enrichGO, Biological Process, Factor 3 of 5")
barplot(ego_BP[[10]], title = "enrichGO, Biological Process, Factor 4 of 5")
barplot(ego_BP[[11]], title = "enrichGO, Biological Process, Factor 5 of 5")
barplot(ego_BP[[12]], title = "enrichGO, Biological Process, Factor 1 of 10")
barplot(ego_BP[[13]], title = "enrichGO, Biological Process, Factor 2 of 10")
barplot(ego_BP[[14]], title = "enrichGO, Biological Process, Factor 3 of 10")
barplot(ego_BP[[15]], title = "enrichGO, Biological Process, Factor 4 of 10")
barplot(ego_BP[[16]], title = "enrichGO, Biological Process, Factor 5 of 10")
barplot(ego_BP[[17]], title = "enrichGO, Biological Process, Factor 6 of 10")
barplot(ego_BP[[18]], title = "enrichGO, Biological Process, Factor 7 of 10")
#barplot(ego_BP[[19]], title = "enrichGO, Biological Process, Factor 8 of 10")
#barplot(ego_BP[[20]], title = "enrichGO, Biological Process, Factor 9 of 10")
#barplot(ego_BP[[21]], title = "enrichGO, Biological Process, Factor 10 of 10")
barplot(ego_CC[[1]], title = "enrichGO, Cellular Component, Factor 1 of 1")
barplot(ego_CC[[2]], title = "enrichGO, Cellular Component, Factor 1 of 2")
barplot(ego_CC[[3]], title = "enrichGO, Cellular Component, Factor 2 of 2")
barplot(ego_CC[[4]], title = "enrichGO, Cellular Component, Factor 1 of 3")
barplot(ego_CC[[5]], title = "enrichGO, Cellular Component, Factor 2 of 3")
#barplot(ego_CC[[6]], title = "enrichGO, Cellular Component, Factor 3 of 3")
barplot(ego_CC[[7]], title = "enrichGO, Cellular Component, Factor 1 of 5")
barplot(ego_CC[[8]], title = "enrichGO, Cellular Component, Factor 2 of 5")
barplot(ego_CC[[9]], title = "enrichGO, Cellular Component, Factor 3 of 5")
barplot(ego_CC[[10]], title = "enrichGO, Cellular Component, Factor 4 of 5")
barplot(ego_CC[[11]], title = "enrichGO, Cellular Component, Factor 5 of 5")
barplot(ego_CC[[12]], title = "enrichGO, Cellular Component, Factor 1 of 10")
barplot(ego_CC[[13]], title = "enrichGO, Cellular Component, Factor 2 of 10")
barplot(ego_CC[[14]], title = "enrichGO, Cellular Component, Factor 3 of 10")
barplot(ego_CC[[15]], title = "enrichGO, Cellular Component, Factor 4 of 10")
barplot(ego_CC[[16]], title = "enrichGO, Cellular Component, Factor 5 of 10")
barplot(ego_CC[[17]], title = "enrichGO, Cellular Component, Factor 6 of 10")
barplot(ego_CC[[18]], title = "enrichGO, Cellular Component, Factor 7 of 10")
#barplot(ego_CC[[19]], title = "enrichGO, Cellular Component, Factor 8 of 10")
#barplot(ego_CC[[20]], title = "enrichGO, Cellular Component, Factor 9 of 10")
#barplot(ego_CC[[21]], title = "enrichGO, Cellular Component, Factor 10 of 10")DAG plots for ego
goplot(ego_MF[[1]]) + labs(title = "enrichGO, Molecular Function, Factor 1 of 1")
goplot(ego_MF[[2]]) + labs(title = "enrichGO, Molecular Function, Factor 1 of 2")
goplot(ego_MF[[3]]) + labs(title = "enrichGO, Molecular Function, Factor 2 of 2")
goplot(ego_MF[[4]]) + labs(title = "enrichGO, Molecular Function, Factor 1 of 3")
goplot(ego_MF[[5]]) + labs(title = "enrichGO, Molecular Function, Factor 2 of 3")
#goplot(ego_MF[[6]]) + labs(title = "enrichGO, Molecular Function, Factor 3 of 3")
goplot(ego_MF[[7]]) + labs(title = "enrichGO, Molecular Function, Factor 1 of 5")
goplot(ego_MF[[8]]) + labs(title = "enrichGO, Molecular Function, Factor 2 of 5")
goplot(ego_MF[[9]]) + labs(title = "enrichGO, Molecular Function, Factor 3 of 5")
#goplot(ego_MF[[10]]) + labs(title = "enrichGO, Molecular Function, Factor 4 of 5")
goplot(ego_MF[[11]]) + labs(title = "enrichGO, Molecular Function, Factor 5 of 5")
goplot(ego_MF[[12]]) + labs(title = "enrichGO, Molecular Function, Factor 1 of 10")
goplot(ego_MF[[13]]) + labs(title = "enrichGO, Molecular Function, Factor 2 of 10")
goplot(ego_MF[[14]]) + labs(title = "enrichGO, Molecular Function, Factor 3 of 10")
goplot(ego_MF[[15]]) + labs(title = "enrichGO, Molecular Function, Factor 4 of 10")
goplot(ego_MF[[16]]) + labs(title = "enrichGO, Molecular Function, Factor 5 of 10")
goplot(ego_MF[[17]]) + labs(title = "enrichGO, Molecular Function, Factor 6 of 10")
goplot(ego_MF[[18]]) + labs(title = "enrichGO, Molecular Function, Factor 7 of 10")
#goplot(ego_MF[[19]]) + labs(title = "enrichGO, Molecular Function, Factor 8 of 10")
#goplot(ego_MF[[20]]) + labs(title = "enrichGO, Molecular Function, Factor 9 of 10")
#goplot(ego_MF[[21]]) + labs(title = "enrichGO, Molecular Function, Factor 10 of 10")
goplot(ego_BP[[1]]) + labs(title = "enrichGO, Biological Process, Factor 1 of 1")
goplot(ego_BP[[2]]) + labs(title = "enrichGO, Biological Process, Factor 1 of 2")
goplot(ego_BP[[3]]) + labs(title = "enrichGO, Biological Process, Factor 2 of 2")
goplot(ego_BP[[4]]) + labs(title = "enrichGO, Biological Process, Factor 1 of 3")
goplot(ego_BP[[5]]) + labs(title = "enrichGO, Biological Process, Factor 2 of 3")
#goplot(ego_BP[[6]]) + labs(title = "enrichGO, Biological Process, Factor 3 of 3")
goplot(ego_BP[[7]]) + labs(title = "enrichGO, Biological Process, Factor 1 of 5")## Warning: ggrepel: 6 unlabeled data points (too many overlaps). Consider
## increasing max.overlaps
goplot(ego_BP[[8]]) + labs(title = "enrichGO, Biological Process, Factor 2 of 5")
goplot(ego_BP[[9]]) + labs(title = "enrichGO, Biological Process, Factor 3 of 5")
goplot(ego_BP[[10]]) + labs(title = "enrichGO, Biological Process, Factor 4 of 5")
goplot(ego_BP[[11]]) + labs(title = "enrichGO, Biological Process, Factor 5 of 5")## Warning: ggrepel: 78 unlabeled data points (too many overlaps). Consider
## increasing max.overlaps
goplot(ego_BP[[12]]) + labs(title = "enrichGO, Biological Process, Factor 1 of 10")
goplot(ego_BP[[13]]) + labs(title = "enrichGO, Biological Process, Factor 2 of 10")
goplot(ego_BP[[14]]) + labs(title = "enrichGO, Biological Process, Factor 3 of 10")
goplot(ego_BP[[15]]) + labs(title = "enrichGO, Biological Process, Factor 4 of 10")
goplot(ego_BP[[16]]) + labs(title = "enrichGO, Biological Process, Factor 5 of 10")## Warning: ggrepel: 2 unlabeled data points (too many overlaps). Consider
## increasing max.overlaps
goplot(ego_BP[[17]]) + labs(title = "enrichGO, Biological Process, Factor 6 of 10")## Warning: ggrepel: 8 unlabeled data points (too many overlaps). Consider
## increasing max.overlaps
goplot(ego_BP[[18]]) + labs(title = "enrichGO, Biological Process, Factor 7 of 10")
#goplot(ego_BP[[19]]) + labs(title = "enrichGO, Biological Process, Factor 8 of 10")
#goplot(ego_BP[[20]]) + labs(title = "enrichGO, Biological Process, Factor 9 of 10")
#goplot(ego_BP[[21]]) + labs(title = "enrichGO, Biological Process, Factor 10 of 10")
goplot(ego_CC[[1]]) + labs(title = "enrichGO, Cellular Component, Factor 1 of 1")
goplot(ego_CC[[2]]) + labs(title = "enrichGO, Cellular Component, Factor 1 of 2")
goplot(ego_CC[[3]]) + labs(title = "enrichGO, Cellular Component, Factor 2 of 2")
goplot(ego_CC[[4]]) + labs(title = "enrichGO, Cellular Component, Factor 1 of 3")
goplot(ego_CC[[5]]) + labs(title = "enrichGO, Cellular Component, Factor 2 of 3")
#goplot(ego_CC[[6]]) + labs(title = "enrichGO, Cellular Component, Factor 3 of 3")
goplot(ego_CC[[7]]) + labs(title = "enrichGO, Cellular Component, Factor 1 of 5")
goplot(ego_CC[[8]]) + labs(title = "enrichGO, Cellular Component, Factor 2 of 5")
goplot(ego_CC[[9]]) + labs(title = "enrichGO, Cellular Component, Factor 3 of 5")
#goplot(ego_CC[[10]]) + labs(title = "enrichGO, Cellular Component, Factor 4 of 5")
goplot(ego_CC[[11]]) + labs(title = "enrichGO, Cellular Component, Factor 5 of 5")
goplot(ego_CC[[12]]) + labs(title = "enrichGO, Cellular Component, Factor 1 of 10")
goplot(ego_CC[[13]]) + labs(title = "enrichGO, Cellular Component, Factor 2 of 10")
goplot(ego_CC[[14]]) + labs(title = "enrichGO, Cellular Component, Factor 3 of 10")
goplot(ego_CC[[15]]) + labs(title = "enrichGO, Cellular Component, Factor 4 of 10")
goplot(ego_CC[[16]]) + labs(title = "enrichGO, Cellular Component, Factor 5 of 10")
goplot(ego_CC[[17]]) + labs(title = "enrichGO, Cellular Component, Factor 6 of 10")
goplot(ego_CC[[18]]) + labs(title = "enrichGO, Cellular Component, Factor 7 of 10")
#goplot(ego_CC[[19]]) + labs(title = "enrichGO, Cellular Component, Factor 8 of 10")
#goplot(ego_CC[[20]]) + labs(title = "enrichGO, Cellular Component, Factor 9 of 10")
#goplot(ego_CC[[21]]) + labs(title = "enrichGO, Cellular Component, Factor 10 of 10")3. Export Pathway Analysis result to data
pathway = list("ggo_MF" = ggo_MF,
"ggo_BP" = ggo_BP,
"ggo_CC" = ggo_CC,
"ego_MF" = ego_MF,
"ego_BP" = ego_BP,
"ego_CC" = ego_CC)
saveRDS(pathway, file = "data/out_pathway/pathways_mofa_extracted_by_bic.rds")